chr17-82237396-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004207.4(SLC16A3):c.626G>A(p.Gly209Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000154 in 1,554,310 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004207.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC16A3 | NM_004207.4 | c.626G>A | p.Gly209Glu | missense_variant | 4/5 | ENST00000582743.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC16A3 | ENST00000582743.6 | c.626G>A | p.Gly209Glu | missense_variant | 4/5 | 1 | NM_004207.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152206Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000308 AC: 5AN: 162458Hom.: 0 AF XY: 0.0000112 AC XY: 1AN XY: 89278
GnomAD4 exome AF: 0.00000785 AC: 11AN: 1401986Hom.: 0 Cov.: 31 AF XY: 0.00000289 AC XY: 2AN XY: 692326
GnomAD4 genome ? AF: 0.0000853 AC: 13AN: 152324Hom.: 1 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.626G>A (p.G209E) alteration is located in exon 4 (coding exon 3) of the SLC16A3 gene. This alteration results from a G to A substitution at nucleotide position 626, causing the glycine (G) at amino acid position 209 to be replaced by a glutamic acid (E). 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