21-44573933-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_198687.2(KRTAP10-4):c.175C>G(p.Pro59Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRTAP10-4 | NM_198687.2 | c.175C>G | p.Pro59Ala | missense_variant | Exon 1 of 1 | ENST00000400374.4 | NP_941960.2 | |
TSPEAR | NM_144991.3 | c.83-5928G>C | intron_variant | Intron 1 of 11 | ENST00000323084.9 | NP_659428.2 | ||
TSPEAR | NM_001272037.2 | c.-122-5928G>C | intron_variant | Intron 2 of 12 | NP_001258966.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRTAP10-4 | ENST00000400374.4 | c.175C>G | p.Pro59Ala | missense_variant | Exon 1 of 1 | 6 | NM_198687.2 | ENSP00000383225.3 | ||
TSPEAR | ENST00000323084.9 | c.83-5928G>C | intron_variant | Intron 1 of 11 | 1 | NM_144991.3 | ENSP00000321987.4 | |||
TSPEAR | ENST00000642437.1 | n.*28-5928G>C | intron_variant | Intron 2 of 12 | ENSP00000496535.1 | |||||
TSPEAR | ENST00000397916.1 | n.-117G>C | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152076Hom.: 0 Cov.: 47
GnomAD3 exomes AF: 0.00000829 AC: 2AN: 241354Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131714
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460404Hom.: 0 Cov.: 233 AF XY: 0.00000275 AC XY: 2AN XY: 726532
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152076Hom.: 0 Cov.: 47 AF XY: 0.0000404 AC XY: 3AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.175C>G (p.P59A) alteration is located in exon 1 (coding exon 1) of the KRTAP10-4 gene. This alteration results from a C to G substitution at nucleotide position 175, causing the proline (P) at amino acid position 59 to be replaced by an alanine (A). 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