rs144755294
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006517.5(SLC16A2):c.949C>T(p.Arg317Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,209,889 control chromosomes in the GnomAD database, including 2 homozygotes. There are 96 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006517.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC16A2 | NM_006517.5 | c.949C>T | p.Arg317Cys | missense_variant | 3/6 | ENST00000587091.6 | NP_006508.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC16A2 | ENST00000587091.6 | c.949C>T | p.Arg317Cys | missense_variant | 3/6 | 1 | NM_006517.5 | ENSP00000465734.1 | ||
SLC16A2 | ENST00000590447.1 | c.388C>T | p.Arg130Cys | missense_variant | 2/4 | 5 | ENSP00000466213.1 | |||
SLC16A2 | ENST00000636771.1 | n.*650C>T | non_coding_transcript_exon_variant | 4/7 | 5 | ENSP00000490445.1 | ||||
SLC16A2 | ENST00000636771.1 | n.*650C>T | 3_prime_UTR_variant | 4/7 | 5 | ENSP00000490445.1 |
Frequencies
GnomAD3 genomes AF: 0.00153 AC: 171AN: 111697Hom.: 1 Cov.: 22 AF XY: 0.00165 AC XY: 56AN XY: 33875
GnomAD3 exomes AF: 0.000328 AC: 60AN: 183191Hom.: 0 AF XY: 0.000148 AC XY: 10AN XY: 67661
GnomAD4 exome AF: 0.000167 AC: 183AN: 1098140Hom.: 1 Cov.: 33 AF XY: 0.000110 AC XY: 40AN XY: 363502
GnomAD4 genome AF: 0.00153 AC: 171AN: 111749Hom.: 1 Cov.: 22 AF XY: 0.00165 AC XY: 56AN XY: 33937
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 08, 2014 | - - |
Spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2018 | This alteration is classified as 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 06, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at