2-27442611-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173853.4(KRTCAP3):c.61G>A(p.Val21Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V21A) has been classified as Uncertain significance.
Frequency
Consequence
NM_173853.4 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 |
---|---|---|---|---|---|---|---|
KRTCAP3 | NM_173853.4 | c.61G>A | p.Val21Met | missense_variant | 2/7 | ENST00000288873.7 | |
KRTCAP3 | NM_001168364.2 | c.61G>A | p.Val21Met | missense_variant | 2/7 | ||
KRTCAP3 | NM_001321325.2 | c.61G>A | p.Val21Met | missense_variant | 2/7 | ||
KRTCAP3 | XM_047443704.1 | c.61G>A | p.Val21Met | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTCAP3 | ENST00000288873.7 | c.61G>A | p.Val21Met | missense_variant | 2/7 | 1 | NM_173853.4 | P1 | |
KRTCAP3 | ENST00000543753.5 | c.61G>A | p.Val21Met | missense_variant | 2/7 | 5 | P1 | ||
KRTCAP3 | ENST00000407293.5 | c.7G>A | p.Val3Met | missense_variant | 1/6 | 2 | |||
KRTCAP3 | ENST00000453171.5 | c.28+171G>A | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1411752Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 697540
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.61G>A (p.V21M) alteration is located in exon 2 (coding exon 2) of the KRTCAP3 gene. This alteration results from a G to A substitution at nucleotide position 61, causing the valine (V) at amino acid position 21 to be replaced by a methionine (M). 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
Publications
No publications associated with this variant yet.