21-44627256-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_198690.3(KRTAP10-9):c.85C>A(p.Pro29Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,612,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P29L) has been classified as Uncertain significance.
Frequency
Consequence
NM_198690.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP10-9 | NM_198690.3 | c.85C>A | p.Pro29Thr | missense_variant | 1/1 | ENST00000397911.5 | |
TSPEAR | NM_144991.3 | c.83-59251G>T | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-59251G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-9 | ENST00000397911.5 | c.85C>A | p.Pro29Thr | missense_variant | 1/1 | NM_198690.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-59251G>T | intron_variant | 1 | NM_144991.3 | P1 | |||
KRTAP10-9 | ENST00000484861.1 | n.134C>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
TSPEAR | ENST00000642437.1 | c.*28-59251G>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000140 AC: 35AN: 249330Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135280
GnomAD4 exome AF: 0.000151 AC: 221AN: 1460338Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 726510
GnomAD4 genome AF: 0.000125 AC: 19AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.85C>A (p.P29T) alteration is located in exon 1 (coding exon 1) of the KRTAP10-9 gene. This alteration results from a C to A substitution at nucleotide position 85, causing the proline (P) at amino acid position 29 to be replaced by a threonine (T). 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