rs148882860
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_139319.3(SLC17A8):c.858T>C(p.Tyr286Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000415 in 1,614,112 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_139319.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC17A8 | NM_139319.3 | c.858T>C | p.Tyr286Tyr | synonymous_variant | Exon 7 of 12 | ENST00000323346.10 | NP_647480.1 | |
SLC17A8 | NM_001145288.2 | c.858T>C | p.Tyr286Tyr | synonymous_variant | Exon 7 of 11 | NP_001138760.1 | ||
LOC124903108 | XR_007063645.1 | n.*184T>C | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC17A8 | ENST00000323346.10 | c.858T>C | p.Tyr286Tyr | synonymous_variant | Exon 7 of 12 | 1 | NM_139319.3 | ENSP00000316909.4 | ||
SLC17A8 | ENST00000392989.3 | c.858T>C | p.Tyr286Tyr | synonymous_variant | Exon 7 of 11 | 1 | ENSP00000376715.3 | |||
SLC17A8 | ENST00000547922.1 | n.-184T>C | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00233 AC: 355AN: 152140Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000606 AC: 152AN: 250764Hom.: 1 AF XY: 0.000524 AC XY: 71AN XY: 135500
GnomAD4 exome AF: 0.000215 AC: 314AN: 1461854Hom.: 3 Cov.: 32 AF XY: 0.000212 AC XY: 154AN XY: 727230
GnomAD4 genome AF: 0.00234 AC: 356AN: 152258Hom.: 3 Cov.: 32 AF XY: 0.00248 AC XY: 185AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:3
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SLC17A8: BP4, BP7, BS1, BS2 -
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not specified Benign:2
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Autosomal dominant nonsyndromic hearing loss 25 Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at