chr21-44592380-G-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.105C>A(p.Asp35Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000512 in 1,562,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 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.105C>A | p.Asp35Glu | missense_variant | 1/1 | ENST00000400368.1 | |
TSPEAR | NM_144991.3 | c.83-24375C>A | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-24375C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-6 | ENST00000400368.1 | c.105C>A | p.Asp35Glu | missense_variant | 1/1 | NM_198688.3 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-24375C>A | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*28-24375C>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000401 AC: 5AN: 124534Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 241120Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130536
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1438400Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1AN XY: 712952
GnomAD4 genome ? AF: 0.0000401 AC: 5AN: 124534Hom.: 0 Cov.: 26 AF XY: 0.0000674 AC XY: 4AN XY: 59356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.105C>A (p.D35E) alteration is located in exon 1 (coding exon 1) of the KRTAP10-6 gene. This alteration results from a C to A substitution at nucleotide position 105, causing the aspartic acid (D) at amino acid position 35 to be replaced by a glutamic acid (E). 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