4-88097565-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004827.3(ABCG2):āc.1535C>Gā(p.Thr512Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000616 in 1,461,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004827.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCG2 | ENST00000237612.8 | c.1535C>G | p.Thr512Ser | missense_variant | Exon 13 of 16 | 1 | NM_004827.3 | ENSP00000237612.3 | ||
ABCG2 | ENST00000515655.5 | c.1535C>G | p.Thr512Ser | missense_variant | Exon 13 of 16 | 1 | ENSP00000426917.1 | |||
ABCG2 | ENST00000650821.1 | c.1535C>G | p.Thr512Ser | missense_variant | Exon 14 of 17 | ENSP00000498246.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251070Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135666
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461836Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727220
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1535C>G (p.T512S) alteration is located in exon 13 (coding exon 12) of the ABCG2 gene. This alteration results from a C to G substitution at nucleotide position 1535, causing the threonine (T) at amino acid position 512 to be replaced by a serine (S). 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