rs6644950
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001636.4(SLC25A6):c.687C>T(p.Tyr229Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,613,348 control chromosomes in the GnomAD database, including 481 homozygotes. There are 11,322 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001636.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A6 | ENST00000381401.11 | c.687C>T | p.Tyr229Tyr | synonymous_variant | Exon 3 of 4 | 1 | NM_001636.4 | ENSP00000370808.5 | ||
SLC25A6 | ENST00000475167.6 | n.880C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 | |||||
SLC25A6 | ENST00000484026.6 | n.*14C>T | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0122 AC: 1850AN: 152194Hom.: 44 Cov.: 33 AF XY: 0.0125 AC XY: 929AN XY: 74340
GnomAD3 exomes AF: 0.0193 AC: 4843AN: 250462Hom.: 173 AF XY: 0.0196 AC XY: 2657AN XY: 135502
GnomAD4 exome AF: 0.0143 AC: 20841AN: 1461036Hom.: 437 Cov.: 41 AF XY: 0.0143 AC XY: 10393AN XY: 726850
GnomAD4 genome AF: 0.0122 AC: 1852AN: 152312Hom.: 44 Cov.: 33 AF XY: 0.0125 AC XY: 929AN XY: 74468
ClinVar
Submissions by phenotype
SLC25A6-related disorder Benign:1
This variant is classified as likely 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