chr6-43301682-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_153320.2(SLC22A7):c.1051G>A(p.Val351Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,609,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_153320.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC22A7 | NM_153320.2 | c.1051G>A | p.Val351Met | missense_variant | 7/11 | ENST00000372585.10 | NP_696961.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A7 | ENST00000372585.10 | c.1051G>A | p.Val351Met | missense_variant | 7/11 | 5 | NM_153320.2 | ENSP00000361666 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000604 AC: 15AN: 248162Hom.: 0 AF XY: 0.0000597 AC XY: 8AN XY: 134044
GnomAD4 exome AF: 0.000101 AC: 147AN: 1457682Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 724476
GnomAD4 genome AF: 0.000217 AC: 33AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at