chr21-44592088-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198688.3(KRTAP10-6):c.397T>A(p.Ser133Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,474,376 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_198688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP10-6 | NM_198688.3 | c.397T>A | p.Ser133Thr | missense_variant | 1/1 | ENST00000400368.1 | |
TSPEAR | NM_144991.3 | c.83-24083T>A | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-24083T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-6 | ENST00000400368.1 | c.397T>A | p.Ser133Thr | missense_variant | 1/1 | NM_198688.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-24083T>A | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*28-24083T>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000244 AC: 3AN: 123100Hom.: 0 Cov.: 22
GnomAD3 exomes AF: 0.00000834 AC: 2AN: 239852Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129816
GnomAD4 exome AF: 0.0000126 AC: 17AN: 1351276Hom.: 1 Cov.: 37 AF XY: 0.00000744 AC XY: 5AN XY: 671958
GnomAD4 genome AF: 0.0000244 AC: 3AN: 123100Hom.: 0 Cov.: 22 AF XY: 0.0000169 AC XY: 1AN XY: 59308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.397T>A (p.S133T) alteration is located in exon 1 (coding exon 1) of the KRTAP10-6 gene. This alteration results from a T to A substitution at nucleotide position 397, causing the serine (S) at amino acid position 133 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