chr19-45364541-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_000400.4(ERCC2):c.601C>T(p.His201Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000319 in 1,613,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000400.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000541 AC: 135AN: 249522Hom.: 0 AF XY: 0.000709 AC XY: 96AN XY: 135390
GnomAD4 exome AF: 0.000323 AC: 472AN: 1460882Hom.: 0 Cov.: 37 AF XY: 0.000424 AC XY: 308AN XY: 726722
GnomAD4 genome AF: 0.000282 AC: 43AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74424
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:3
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Xeroderma pigmentosum, group D Uncertain:1
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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Xeroderma pigmentosum Benign:1
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ERCC2-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at