X-24693978-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001330360.2(POLA1):c.17G>A(p.Gly6Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000838 in 1,193,917 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330360.2 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: 0.00000882 AC: 1AN: 113433Hom.: 0 Cov.: 24 AF XY: 0.0000281 AC XY: 1AN XY: 35559
GnomAD3 exomes AF: 0.0000339 AC: 5AN: 147300Hom.: 0 AF XY: 0.0000223 AC XY: 1AN XY: 44900
GnomAD4 exome AF: 0.00000833 AC: 9AN: 1080484Hom.: 0 Cov.: 29 AF XY: 0.0000114 AC XY: 4AN XY: 351822
GnomAD4 genome AF: 0.00000882 AC: 1AN: 113433Hom.: 0 Cov.: 24 AF XY: 0.0000281 AC XY: 1AN XY: 35559
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 03, 2022 | This variant has not been reported in the literature in individuals affected with POLA1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 6 of the POLA1 protein (p.Gly6Asp). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at