chr11-1584931-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001005922.1(KRTAP5-1):āc.319G>Cā(p.Gly107Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 8)
Exomes š: 0.000024 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KRTAP5-1
NM_001005922.1 missense
NM_001005922.1 missense
Scores
1
4
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
KRTAP5-1 (HGNC:23596): (keratin associated protein 5-1) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.13535509).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP5-1 | NM_001005922.1 | c.319G>C | p.Gly107Arg | missense_variant | 1/1 | ENST00000382171.2 | |
KRTAP5-AS1 | NR_021489.2 | n.328+11863C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP5-1 | ENST00000382171.2 | c.319G>C | p.Gly107Arg | missense_variant | 1/1 | NM_001005922.1 | P1 | ||
KRTAP5-AS1 | ENST00000424148.1 | n.328+11863C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 8
GnomAD3 genomes
Cov.:
8
GnomAD3 exomes AF: 0.0000730 AC: 17AN: 232816Hom.: 1 AF XY: 0.0000869 AC XY: 11AN XY: 126570
GnomAD3 exomes
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000240 AC: 29AN: 1207372Hom.: 0 Cov.: 48 AF XY: 0.0000334 AC XY: 20AN XY: 598186
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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29
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1207372
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48
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AN XY:
598186
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GnomAD4 genome Cov.: 8
GnomAD4 genome
Cov.:
8
ExAC
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8
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Uncertain
T
Polyphen
D
Vest4
MutPred
Loss of glycosylation at S105 (P = 0.0857);
MVP
MPC
ClinPred
T
GERP RS
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