rs72552713
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004827.3(ABCG2):c.376C>T(p.Gln126Ter) variant causes a stop gained, splice region change. The variant allele was found at a frequency of 0.000377 in 1,611,534 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as association (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004827.3 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCG2 | NM_004827.3 | c.376C>T | p.Gln126Ter | stop_gained, splice_region_variant | 4/16 | ENST00000237612.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCG2 | ENST00000237612.8 | c.376C>T | p.Gln126Ter | stop_gained, splice_region_variant | 4/16 | 1 | NM_004827.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000396 AC: 99AN: 250314Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135252
GnomAD4 exome AF: 0.000392 AC: 572AN: 1459228Hom.: 9 Cov.: 30 AF XY: 0.000375 AC XY: 272AN XY: 725954
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74472
ClinVar
Submissions by phenotype
Uric acid concentration, serum, quantitative trait locus 1 Other:1
association, no assertion criteria provided | literature only | OMIM | Jan 15, 2012 | - - |
Blood group, Junior system Other:1
association, no assertion criteria provided | literature only | OMIM | Oct 22, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at