chr12-21306942-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001386879.1(SLCO1A2):c.382A>T(p.Asn128Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 1,613,300 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001386879.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1A2 | NM_001386879.1 | c.382A>T | p.Asn128Tyr | missense_variant | 5/15 | ENST00000683939.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1A2 | ENST00000683939.1 | c.382A>T | p.Asn128Tyr | missense_variant | 5/15 | NM_001386879.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00561 AC: 854AN: 152108Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00168 AC: 423AN: 251292Hom.: 8 AF XY: 0.00126 AC XY: 171AN XY: 135804
GnomAD4 exome AF: 0.000673 AC: 983AN: 1461074Hom.: 7 Cov.: 30 AF XY: 0.000619 AC XY: 450AN XY: 726800
GnomAD4 genome ? AF: 0.00562 AC: 855AN: 152226Hom.: 9 Cov.: 32 AF XY: 0.00543 AC XY: 404AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at