chr1-19308211-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003689.4(AKR7A2):c.538G>A(p.Glu180Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,614,086 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_003689.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AKR7A2 | NM_003689.4 | c.538G>A | p.Glu180Lys | missense_variant | Exon 3 of 7 | ENST00000235835.8 | NP_003680.2 | |
AKR7A2 | XM_047433095.1 | c.538G>A | p.Glu180Lys | missense_variant | Exon 3 of 4 | XP_047289051.1 | ||
AKR7A2 | NM_001320979.1 | c.486+244G>A | intron_variant | Intron 2 of 5 | NP_001307908.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0117 AC: 1781AN: 152142Hom.: 41 Cov.: 33
GnomAD3 exomes AF: 0.00305 AC: 766AN: 251462Hom.: 19 AF XY: 0.00205 AC XY: 279AN XY: 135904
GnomAD4 exome AF: 0.00111 AC: 1626AN: 1461826Hom.: 23 Cov.: 31 AF XY: 0.000942 AC XY: 685AN XY: 727206
GnomAD4 genome AF: 0.0117 AC: 1785AN: 152260Hom.: 41 Cov.: 33 AF XY: 0.0105 AC XY: 783AN XY: 74442
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