chr21-44637665-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_181688.3(KRTAP10-10):c.248A>C(p.Asp83Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,574,330 control chromosomes in the GnomAD database, including 105 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_181688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP10-10 | NM_181688.3 | c.248A>C | p.Asp83Ala | missense_variant | 1/1 | ENST00000380095.2 | |
TSPEAR | NM_144991.3 | c.83-69660T>G | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-123+52880T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-10 | ENST00000380095.2 | c.248A>C | p.Asp83Ala | missense_variant | 1/1 | NM_181688.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-69660T>G | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*27+52880T>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0147 AC: 2191AN: 148578Hom.: 37 Cov.: 33
GnomAD3 exomes AF: 0.00397 AC: 996AN: 250568Hom.: 21 AF XY: 0.00295 AC XY: 400AN XY: 135510
GnomAD4 exome AF: 0.00164 AC: 2340AN: 1425636Hom.: 67 Cov.: 135 AF XY: 0.00150 AC XY: 1063AN XY: 708420
GnomAD4 genome ? AF: 0.0148 AC: 2199AN: 148694Hom.: 38 Cov.: 33 AF XY: 0.0139 AC XY: 1005AN XY: 72534
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 29, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at