chr11-1607869-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001012708.2(KRTAP5-3):c.517C>T(p.Pro173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000137 in 1,600,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 29)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
KRTAP5-3
NM_001012708.2 missense
NM_001012708.2 missense
Scores
1
2
14
Clinical Significance
Conservation
PhyloP100: 0.0330
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0326021).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRTAP5-3 | NM_001012708.2 | c.517C>T | p.Pro173Ser | missense_variant | 1/1 | ENST00000399685.1 | NP_001012726.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRTAP5-3 | ENST00000399685.1 | c.517C>T | p.Pro173Ser | missense_variant | 1/1 | 6 | NM_001012708.2 | ENSP00000382592.1 |
Frequencies
GnomAD3 genomes AF: 0.000166 AC: 25AN: 150496Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251096Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135744
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GnomAD4 exome AF: 0.000134 AC: 195AN: 1450224Hom.: 0 Cov.: 137 AF XY: 0.000164 AC XY: 118AN XY: 721078
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GnomAD4 genome AF: 0.000166 AC: 25AN: 150496Hom.: 0 Cov.: 29 AF XY: 0.000150 AC XY: 11AN XY: 73320
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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 | Apr 24, 2023 | The c.517C>T (p.P173S) alteration is located in exon 1 (coding exon 1) of the KRTAP5-3 gene. This alteration results from a C to T substitution at nucleotide position 517, causing the proline (P) at amino acid position 173 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
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
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 6
Find out detailed SpliceAI scores and Pangolin per-transcript scores at