6-151615542-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025059.4(CCDC170):c.1810G>A(p.Val604Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,613,434 control chromosomes in the GnomAD database, including 89,807 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_025059.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.356 AC: 54147AN: 151926Hom.: 10397 Cov.: 32
GnomAD3 exomes AF: 0.308 AC: 76889AN: 249358Hom.: 12736 AF XY: 0.311 AC XY: 42139AN XY: 135294
GnomAD4 exome AF: 0.325 AC: 475628AN: 1461390Hom.: 79392 Cov.: 35 AF XY: 0.326 AC XY: 236981AN XY: 727036
GnomAD4 genome AF: 0.356 AC: 54199AN: 152044Hom.: 10415 Cov.: 32 AF XY: 0.348 AC XY: 25889AN XY: 74314
ClinVar
Submissions by phenotype
Estrogen resistance syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Department of Breast and Endocrine Surgery, Kumamoto University | Mar 01, 2014 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.51, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at