2-27442591-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173853.4(KRTCAP3):c.41G>T(p.Gly14Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000326 in 1,535,208 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Consequence
KRTCAP3
NM_173853.4 missense
NM_173853.4 missense
Scores
2
8
9
Clinical Significance
Conservation
PhyloP100: 7.28
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTCAP3 | NM_173853.4 | c.41G>T | p.Gly14Val | missense_variant | 2/7 | ENST00000288873.7 | |
KRTCAP3 | NM_001168364.2 | c.41G>T | p.Gly14Val | missense_variant | 2/7 | ||
KRTCAP3 | NM_001321325.2 | c.41G>T | p.Gly14Val | missense_variant | 2/7 | ||
KRTCAP3 | XM_047443704.1 | c.41G>T | p.Gly14Val | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTCAP3 | ENST00000288873.7 | c.41G>T | p.Gly14Val | missense_variant | 2/7 | 1 | NM_173853.4 | P1 | |
KRTCAP3 | ENST00000543753.5 | c.41G>T | p.Gly14Val | missense_variant | 2/7 | 5 | P1 | ||
KRTCAP3 | ENST00000407293.5 | c.-14G>T | 5_prime_UTR_variant | 1/6 | 2 | ||||
KRTCAP3 | ENST00000453171.5 | c.28+151G>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000259 AC: 4AN: 154628Hom.: 0 AF XY: 0.0000119 AC XY: 1AN XY: 84058
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GnomAD4 exome AF: 0.00000217 AC: 3AN: 1383076Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 681244
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.41G>T (p.G14V) alteration is located in exon 2 (coding exon 2) of the KRTCAP3 gene. This alteration results from a G to T substitution at nucleotide position 41, causing the glycine (G) at amino acid position 14 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
T;T
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at