chr21-44627283-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198690.3(KRTAP10-9):c.112G>A(p.Ala38Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,612,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198690.3 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 |
---|---|---|---|---|---|---|---|
KRTAP10-9 | NM_198690.3 | c.112G>A | p.Ala38Thr | missense_variant | 1/1 | ENST00000397911.5 | |
TSPEAR | NM_144991.3 | c.83-59278C>T | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-59278C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-9 | ENST00000397911.5 | c.112G>A | p.Ala38Thr | missense_variant | 1/1 | NM_198690.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-59278C>T | intron_variant | 1 | NM_144991.3 | P1 | |||
KRTAP10-9 | ENST00000484861.1 | n.161G>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
TSPEAR | ENST00000642437.1 | c.*28-59278C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152060Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000105 AC: 26AN: 248634Hom.: 0 AF XY: 0.0000667 AC XY: 9AN XY: 134994
GnomAD4 exome AF: 0.000115 AC: 168AN: 1460230Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 726458
GnomAD4 genome AF: 0.000112 AC: 17AN: 152060Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.112G>A (p.A38T) alteration is located in exon 1 (coding exon 1) of the KRTAP10-9 gene. This alteration results from a G to A substitution at nucleotide position 112, causing the alanine (A) at amino acid position 38 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