chr21-44573804-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198687.2(KRTAP10-4):c.46C>T(p.Leu16Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,614,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198687.2 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 |
---|---|---|---|---|---|---|---|
KRTAP10-4 | NM_198687.2 | c.46C>T | p.Leu16Phe | missense_variant | 1/1 | ENST00000400374.4 | |
TSPEAR | NM_144991.3 | c.83-5799G>A | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-122-5799G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP10-4 | ENST00000400374.4 | c.46C>T | p.Leu16Phe | missense_variant | 1/1 | NM_198687.2 | P1 | ||
TSPEAR | ENST00000323084.9 | c.83-5799G>A | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000397916.1 | n.13G>A | non_coding_transcript_exon_variant | 1/11 | 1 | ||||
TSPEAR | ENST00000642437.1 | c.*28-5799G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152244Hom.: 0 Cov.: 41
GnomAD3 exomes AF: 0.0000922 AC: 23AN: 249436Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135320
GnomAD4 exome AF: 0.000112 AC: 164AN: 1461844Hom.: 0 Cov.: 195 AF XY: 0.0000935 AC XY: 68AN XY: 727222
GnomAD4 genome AF: 0.000105 AC: 16AN: 152244Hom.: 0 Cov.: 41 AF XY: 0.0000807 AC XY: 6AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2023 | The c.46C>T (p.L16F) alteration is located in exon 1 (coding exon 1) of the KRTAP10-4 gene. This alteration results from a C to T substitution at nucleotide position 46, causing the leucine (L) at amino acid position 16 to be replaced by a phenylalanine (F). 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