rs939885
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152672.6(SLC51A):c.604G>A(p.Val202Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 1,613,134 control chromosomes in the GnomAD database, including 188,626 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_152672.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC51A | NM_152672.6 | c.604G>A | p.Val202Ile | missense_variant | 6/9 | ENST00000296327.10 | |
SLC51A | XM_047447662.1 | c.256G>A | p.Val86Ile | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC51A | ENST00000296327.10 | c.604G>A | p.Val202Ile | missense_variant | 6/9 | 1 | NM_152672.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.428 AC: 65047AN: 151850Hom.: 15243 Cov.: 32
GnomAD3 exomes AF: 0.488 AC: 122599AN: 251448Hom.: 31592 AF XY: 0.484 AC XY: 65839AN XY: 135904
GnomAD4 exome AF: 0.482 AC: 703960AN: 1461166Hom.: 173369 Cov.: 42 AF XY: 0.480 AC XY: 348732AN XY: 726908
GnomAD4 genome ? AF: 0.428 AC: 65092AN: 151968Hom.: 15257 Cov.: 32 AF XY: 0.434 AC XY: 32209AN XY: 74294
ClinVar
Submissions by phenotype
SLC51A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 22, 2023 | This variant is classified as 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