rs34691037
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001282629.2(GBGT1):c.677C>T(p.Thr226Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00494 in 1,609,570 control chromosomes in the GnomAD database, including 303 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001282629.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBGT1 | ENST00000372040.9 | c.696C>T | p.Tyr232Tyr | synonymous_variant | Exon 7 of 7 | 1 | NM_021996.6 | ENSP00000361110.3 | ||
ENSG00000285245 | ENST00000647146.1 | c.396+1253C>T | intron_variant | Intron 6 of 22 | ENSP00000493691.1 |
Frequencies
GnomAD3 genomes AF: 0.0251 AC: 3821AN: 152196Hom.: 162 Cov.: 32
GnomAD3 exomes AF: 0.00685 AC: 1714AN: 250390Hom.: 59 AF XY: 0.00501 AC XY: 679AN XY: 135406
GnomAD4 exome AF: 0.00283 AC: 4121AN: 1457256Hom.: 140 Cov.: 32 AF XY: 0.00244 AC XY: 1766AN XY: 723940
GnomAD4 genome AF: 0.0251 AC: 3824AN: 152314Hom.: 163 Cov.: 32 AF XY: 0.0241 AC XY: 1793AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at