21-44654569-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198698.1(KRTAP12-4):c.46G>T(p.Gly16Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000368 in 1,604,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198698.1 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 |
---|---|---|---|---|---|---|---|
KRTAP12-4 | NM_198698.1 | c.46G>T | p.Gly16Cys | missense_variant | 1/1 | ENST00000391618.1 | |
TSPEAR | NM_144991.3 | c.82+56864G>T | intron_variant | ENST00000323084.9 | |||
TSPEAR | NM_001272037.2 | c.-123+35976G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP12-4 | ENST00000391618.1 | c.46G>T | p.Gly16Cys | missense_variant | 1/1 | NM_198698.1 | P1 | ||
TSPEAR | ENST00000323084.9 | c.82+56864G>T | intron_variant | 1 | NM_144991.3 | P1 | |||
TSPEAR | ENST00000642437.1 | c.*27+35976G>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000213 AC: 5AN: 234274Hom.: 0 AF XY: 0.0000236 AC XY: 3AN XY: 127382
GnomAD4 exome AF: 0.0000262 AC: 38AN: 1452612Hom.: 0 Cov.: 35 AF XY: 0.0000263 AC XY: 19AN XY: 721544
GnomAD4 genome AF: 0.000138 AC: 21AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.46G>T (p.G16C) alteration is located in exon 1 (coding exon 1) of the KRTAP12-4 gene. This alteration results from a G to T substitution at nucleotide position 46, causing the glycine (G) at amino acid position 16 to be replaced by a cysteine (C). 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