chr3-196216721-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_152672.6(SLC51A):c.9G>A(p.Pro3Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000099 in 1,575,280 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_152672.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 151982Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000215 AC: 40AN: 185998Hom.: 0 AF XY: 0.000169 AC XY: 17AN XY: 100796
GnomAD4 exome AF: 0.0000618 AC: 88AN: 1423180Hom.: 1 Cov.: 33 AF XY: 0.0000539 AC XY: 38AN XY: 704498
GnomAD4 genome AF: 0.000447 AC: 68AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74360
ClinVar
Submissions by phenotype
SLC51A-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