21-44591665-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198688.3(KRTAP10-6):c.820G>A(p.Val274Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,585,064 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRTAP10-6 | NM_198688.3 | c.820G>A | p.Val274Ile | missense_variant | Exon 1 of 1 | ENST00000400368.1 | NP_941961.3 | |
TSPEAR | NM_144991.3 | c.83-23660G>A | intron_variant | Intron 1 of 11 | ENST00000323084.9 | NP_659428.2 | ||
TSPEAR | NM_001272037.2 | c.-122-23660G>A | intron_variant | Intron 2 of 12 | NP_001258966.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRTAP10-6 | ENST00000400368.1 | c.820G>A | p.Val274Ile | missense_variant | Exon 1 of 1 | 6 | NM_198688.3 | ENSP00000383219.1 | ||
TSPEAR | ENST00000323084.9 | c.83-23660G>A | intron_variant | Intron 1 of 11 | 1 | NM_144991.3 | ENSP00000321987.4 | |||
TSPEAR | ENST00000642437.1 | n.*28-23660G>A | intron_variant | Intron 2 of 12 | ENSP00000496535.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151438Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251276Hom.: 1 AF XY: 0.0000736 AC XY: 10AN XY: 135816
GnomAD4 exome AF: 0.000295 AC: 423AN: 1433626Hom.: 2 Cov.: 143 AF XY: 0.000244 AC XY: 174AN XY: 712838
GnomAD4 genome AF: 0.000112 AC: 17AN: 151438Hom.: 0 Cov.: 32 AF XY: 0.0000541 AC XY: 4AN XY: 73950
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at