1-45331480-C-T

Variant names:

• chr1-45331480-C-T
• rs878854184
• NM_001048174.2:c.1179G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2 BP4_Moderate BP6_Very_Strong BP7

The NM_001048174.2(MUTYH):​c.1179G>A​(p.Leu393Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L393L) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MUTYH NM_001048174.2 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.226
• Publications: 1 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 -9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.019).
• BP6: Variant 1-45331480-C-T is Benign according to our data. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45331480-C-T is described in CliVar as Likely_benign. Clinvar id is 238335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.226 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUTYH	NM_001048174.2	c.1179G>A	p.Leu393Leu	synonymous_variant	Exon 13 of 16	ENST00000456914.7	NP_001041639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUTYH	ENST00000456914.7	c.1179G>A	p.Leu393Leu	synonymous_variant	Exon 13 of 16	1	NM_001048174.2	ENSP00000407590.2
ENSG00000288208	ENST00000671898.1	n.1767G>A		non_coding_transcript_exon_variant	Exon 17 of 21			ENSP00000499896.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152268 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461838 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727216

African (AFR) AF: 0.0000597 AC: 2 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53378

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5766

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1112006

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152268 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74388

African (AFR) AF: 0.0000241 AC: 1 AN: 41476

American (AMR) AF: 0.00 AC: 0 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.00 AC: 0 AN: 4836

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10632

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68046

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000151

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Sep 15, 2017

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Familial adenomatous polyposis 2 Benign:1

Aug 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:1

Nov 03, 2017

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	0.94
DANN	Benign	0.80
PhyloP100		-0.23
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs878854184; hg19: chr1-45797152;