chr1-45331583-G-A

Variant names:

• chr1-45331583-G-A
• rs3219490
• NM_001048174.2:c.1103-27C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BS2_Supporting

The NM_001048174.2(MUTYH):​c.1103-27C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00425 in 1,613,578 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0030 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0044 (17 hom.)
• Consequence: MUTYH NM_001048174.2 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8
• Conservation: PhyloP100: -0.676
• Publications: 6 publications found

Genes affected

MUTYH (HGNC:7527): (mutY DNA glycosylase) This gene encodes a DNA glycosylase involved in oxidative DNA damage repair. The enzyme excises adenine bases from the DNA backbone at sites where adenine is inappropriately paired with guanine, cytosine, or 8-oxo-7,8-dihydroguanine, a major oxidatively damaged DNA lesion. The protein is localized to the nucleus and mitochondria. This gene product is thought to play a role in signaling apoptosis by the introduction of single-strand breaks following oxidative damage. Mutations in this gene result in heritable predisposition to colorectal cancer, termed MUTYH-associated polyposis (MAP). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]

MUTYH Gene-Disease associations (from GenCC):

• familial adenomatous polyposis 2

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen, G2P
• colorectal cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
• familial ovarian cancer

  Inheritance: AD, AR Classification: NO_KNOWN Submitted by: ClinGen
• hereditary breast carcinoma

  Inheritance: AD, AR Classification: NO_KNOWN Submitted by: ClinGen

ENSG00000288208 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-45331583-G-A is Benign according to our data. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331583-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 801475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAdExome4 at 17 AD,AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUTYH	NM_001048174.2	c.1103-27C>T		intron_variant	Intron 12 of 15	ENST00000456914.7	NP_001041639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUTYH	ENST00000456914.7	c.1103-27C>T		intron_variant	Intron 12 of 15	1	NM_001048174.2	ENSP00000407590.2
ENSG00000288208	ENST00000671898.1	n.1691-27C>T		intron_variant	Intron 16 of 20			ENSP00000499896.1

Frequencies

GnomAD3 genomes AF: 0.00300 AC: 456 AN: 152242 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00268

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00492

Gnomad OTH AF: 0.00621

GnomAD2 exomes AF: 0.00365 AC: 908 AN: 248612 AF XY: 0.00380

Gnomad AFR exome AF: 0.00109

Gnomad AMR exome AF: 0.00301

Gnomad ASJ exome AF: 0.00379

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000525

Gnomad NFE exome AF: 0.00577

Gnomad OTH exome AF: 0.00280

GnomAD4 exome AF: 0.00438 AC: 6406 AN: 1461218 Hom.: 17 Cov.: 33 AF XY: 0.00443 AC XY: 3222 AN XY: 726876

African (AFR) AF: 0.000597 AC: 20 AN: 33480

American (AMR) AF: 0.00295 AC: 132 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00363 AC: 95 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00242 AC: 209 AN: 86258

European-Finnish (FIN) AF: 0.000455 AC: 24 AN: 52782

Middle Eastern (MID) AF: 0.00607 AC: 35 AN: 5768

European-Non Finnish (NFE) AF: 0.00506 AC: 5626 AN: 1111986

Other (OTH) AF: 0.00439 AC: 265 AN: 60386

GnomAD4 genome AF: 0.00299 AC: 456 AN: 152360 Hom.: 0 Cov.: 33 AF XY: 0.00281 AC XY: 209 AN XY: 74506

African (AFR) AF: 0.00103 AC: 43 AN: 41588

American (AMR) AF: 0.00268 AC: 41 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00492 AC: 335 AN: 68036

Other (OTH) AF: 0.00614 AC: 13 AN: 2116

Alfa AF: 0.00447 Hom.: 0

Bravo AF: 0.00320

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Apr 10, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MUTYH: BS1, BS2 -

Jun 24, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 17949294, 15943555, 17524638, 16774938, 16616356, 16557584, 22297469, 20191381, 21777424, 27829682) -

Familial adenomatous polyposis 2 Benign:2

May 28, 2019

Mendelics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

MUTYH-related disorder Benign:1

Dec 02, 2021

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Hereditary cancer-predisposing syndrome Benign:1

Jul 29, 2021

Sema4, Sema4

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: curation

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3219490; hg19: chr1-45797255; COSMIC: COSV104641844;