chr6-25762027-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005495.3(SLC17A4):c.65T>G(p.Val22Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,308 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V22M) has been classified as Likely benign.
Frequency
Consequence
NM_005495.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC17A4 | NM_005495.3 | c.65T>G | p.Val22Gly | missense_variant | 2/12 | ENST00000377905.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC17A4 | ENST00000377905.9 | c.65T>G | p.Val22Gly | missense_variant | 2/12 | 1 | NM_005495.3 | P1 | |
SLC17A4 | ENST00000397076.2 | c.-198T>G | 5_prime_UTR_variant | 1/7 | 2 | ||||
SLC17A4 | ENST00000439485.6 | c.-198T>G | 5_prime_UTR_variant | 2/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250790Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135534
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1461194Hom.: 0 Cov.: 30 AF XY: 0.0000482 AC XY: 35AN XY: 726888
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.65T>G (p.V22G) alteration is located in exon 2 (coding exon 1) of the SLC17A4 gene. This alteration results from a T to G substitution at nucleotide position 65, causing the valine (V) at amino acid position 22 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at