1-45330443-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001048174.2(MUTYH):c.1434+73C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,470,990 control chromosomes in the GnomAD database, including 2,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.066 ( 1173 hom., cov: 30)
Exomes 𝑓: 0.0067 ( 881 hom. )
Consequence
MUTYH
NM_001048174.2 intron
NM_001048174.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.212
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 1-45330443-G-A is Benign according to our data. Variant chr1-45330443-G-A is described in ClinVar as [Benign]. Clinvar id is 1260412.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUTYH | NM_001048174.2 | c.1434+73C>T | intron_variant | ENST00000456914.7 | |||
MUTYH | NM_001128425.2 | c.1518+73C>T | intron_variant | ENST00000710952.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUTYH | ENST00000456914.7 | c.1434+73C>T | intron_variant | 1 | NM_001048174.2 | A1 | |||
MUTYH | ENST00000710952.2 | c.1518+73C>T | intron_variant | NM_001128425.2 |
Frequencies
GnomAD3 genomes AF: 0.0663 AC: 10068AN: 151814Hom.: 1174 Cov.: 30
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GnomAD4 exome AF: 0.00671 AC: 8851AN: 1319058Hom.: 881 AF XY: 0.00584 AC XY: 3838AN XY: 657010
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GnomAD4 genome AF: 0.0663 AC: 10068AN: 151932Hom.: 1173 Cov.: 30 AF XY: 0.0647 AC XY: 4802AN XY: 74254
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at