rs201362069
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_198688.3(KRTAP10-6):c.107A>C(p.Asp36Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,521,062 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198688.3 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 |
---|---|---|---|---|---|---|---|
KRTAP10-6 | NM_198688.3 | c.107A>C | p.Asp36Ala | missense_variant | 1/1 | ENST00000400368.1 | |
TSPEAR | NM_144991.3 | c.83-24373A>C | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-24373A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-6 | ENST00000400368.1 | c.107A>C | p.Asp36Ala | missense_variant | 1/1 | NM_198688.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-24373A>C | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*28-24373A>C | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00580 AC: 672AN: 115942Hom.: 7 Cov.: 24
GnomAD3 exomes AF: 0.00946 AC: 2271AN: 240130Hom.: 3 AF XY: 0.00932 AC XY: 1211AN XY: 129972
GnomAD4 exome AF: 0.00141 AC: 1975AN: 1405010Hom.: 92 Cov.: 33 AF XY: 0.00135 AC XY: 943AN XY: 696404
GnomAD4 genome ? AF: 0.00580 AC: 673AN: 116052Hom.: 7 Cov.: 24 AF XY: 0.00574 AC XY: 317AN XY: 55206
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 12, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at