rs13337489
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004996.4(ABCC1):c.3140G>A(p.Cys1047Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,610,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C1047S) has been classified as Likely benign.
Frequency
Consequence
NM_004996.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC1 | NM_004996.4 | c.3140G>A | p.Cys1047Tyr | missense_variant | 23/31 | ENST00000399410.8 | NP_004987.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC1 | ENST00000399410.8 | c.3140G>A | p.Cys1047Tyr | missense_variant | 23/31 | 1 | NM_004996.4 | ENSP00000382342.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247766Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134586
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1458544Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 724774
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at