chr21-44592154-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.331G>A(p.Val111Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000282 in 1,563,524 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP10-6 | NM_198688.3 | c.331G>A | p.Val111Met | missense_variant | 1/1 | ENST00000400368.1 | |
TSPEAR | NM_144991.3 | c.83-24149G>A | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-24149G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-6 | ENST00000400368.1 | c.331G>A | p.Val111Met | missense_variant | 1/1 | NM_198688.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-24149G>A | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*28-24149G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000983 AC: 135AN: 137348Hom.: 0 Cov.: 20
GnomAD3 exomes AF: 0.000460 AC: 110AN: 238972Hom.: 6 AF XY: 0.000400 AC XY: 52AN XY: 130034
GnomAD4 exome AF: 0.000215 AC: 306AN: 1426062Hom.: 2 Cov.: 36 AF XY: 0.000216 AC XY: 153AN XY: 709708
GnomAD4 genome ? AF: 0.000982 AC: 135AN: 137462Hom.: 0 Cov.: 20 AF XY: 0.000871 AC XY: 58AN XY: 66628
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | KRTAP10-6: BP4, BS2; TSPEAR: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at