rs3219466
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001128425.2(MUTYH):c.-127C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 1,553,774 control chromosomes in the GnomAD database, including 862 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001128425.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TOE1 | ENST00000372090.6 | c.52+77G>A | intron_variant | Intron 1 of 7 | 1 | NM_025077.4 | ENSP00000361162.5 | |||
ENSG00000288208 | ENST00000671898.1 | n.541-5870C>T | intron_variant | Intron 5 of 20 | ENSP00000499896.1 |
Frequencies
GnomAD3 genomes AF: 0.0215 AC: 3279AN: 152226Hom.: 59 Cov.: 32
GnomAD4 exome AF: 0.0317 AC: 44373AN: 1401430Hom.: 803 Cov.: 33 AF XY: 0.0316 AC XY: 21841AN XY: 691954
GnomAD4 genome AF: 0.0215 AC: 3278AN: 152344Hom.: 59 Cov.: 32 AF XY: 0.0207 AC XY: 1539AN XY: 74490
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
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There is insufficient or conflicting evidence for classification of this alteration. -
Familial adenomatous polyposis 2 Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at