chr17-40999708-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031959.3(KRTAP3-2):āc.146A>Gā(p.Asp49Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000316 in 1,613,940 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D49N) has been classified as Uncertain significance.
Frequency
Consequence
NM_031959.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP3-2 | NM_031959.3 | c.146A>G | p.Asp49Gly | missense_variant | 1/1 | ENST00000391587.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP3-2 | ENST00000391587.3 | c.146A>G | p.Asp49Gly | missense_variant | 1/1 | NM_031959.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151996Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251170Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135844
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461826Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727212
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.146A>G (p.D49G) alteration is located in exon 1 (coding exon 1) of the KRTAP3-2 gene. This alteration results from a A to G substitution at nucleotide position 146, causing the aspartic acid (D) at amino acid position 49 to be replaced by a glycine (G). 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