chr21-44573796-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198687.2(KRTAP10-4):c.38G>A(p.Arg13His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000384 in 1,613,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198687.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP10-4 | NM_198687.2 | c.38G>A | p.Arg13His | missense_variant | 1/1 | ENST00000400374.4 | |
TSPEAR | NM_144991.3 | c.83-5791C>T | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-5791C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-4 | ENST00000400374.4 | c.38G>A | p.Arg13His | missense_variant | 1/1 | NM_198687.2 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-5791C>T | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000397916.1 | n.21C>T | non_coding_transcript_exon_variant | 1/11 | 1 | ||||
TSPEAR | ENST00000642437.1 | c.*28-5791C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152158Hom.: 0 Cov.: 41
GnomAD3 exomes AF: 0.000345 AC: 86AN: 249450Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135328
GnomAD4 exome AF: 0.000398 AC: 581AN: 1461572Hom.: 0 Cov.: 195 AF XY: 0.000410 AC XY: 298AN XY: 727076
GnomAD4 genome AF: 0.000250 AC: 38AN: 152276Hom.: 0 Cov.: 41 AF XY: 0.000201 AC XY: 15AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.38G>A (p.R13H) alteration is located in exon 1 (coding exon 1) of the KRTAP10-4 gene. This alteration results from a G to A substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at