12-52286388-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002281.4(KRT81):c.1385C>T(p.Ala462Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00419 in 1,555,306 control chromosomes in the GnomAD database, including 222 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A462E) has been classified as Uncertain significance.
Frequency
Consequence
NM_002281.4 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 |
---|---|---|---|---|---|---|---|
KRT81 | NM_002281.4 | c.1385C>T | p.Ala462Val | missense_variant | 9/9 | ENST00000327741.9 | |
KRT86 | NM_001320198.2 | c.-5+10442G>A | intron_variant | ENST00000423955.7 | |||
KRT81 | XM_047428838.1 | c.1385C>T | p.Ala462Val | missense_variant | 10/10 | ||
KRT86 | XM_005268866.5 | c.129+10442G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT81 | ENST00000327741.9 | c.1385C>T | p.Ala462Val | missense_variant | 9/9 | 1 | NM_002281.4 | P1 | |
KRT86 | ENST00000423955.7 | c.-5+10442G>A | intron_variant | 2 | NM_001320198.2 | P1 | |||
KRT86 | ENST00000553310.6 | c.-4-15525G>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0217 AC: 3298AN: 152176Hom.: 118 Cov.: 33
GnomAD3 exomes AF: 0.00521 AC: 824AN: 158094Hom.: 25 AF XY: 0.00369 AC XY: 309AN XY: 83656
GnomAD4 exome AF: 0.00229 AC: 3212AN: 1403012Hom.: 102 Cov.: 33 AF XY: 0.00197 AC XY: 1361AN XY: 692386
GnomAD4 genome ? AF: 0.0217 AC: 3310AN: 152294Hom.: 120 Cov.: 33 AF XY: 0.0210 AC XY: 1567AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at