rs77039648
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001001480.3(KRTAP5-5):āc.575A>Gā(p.Tyr192Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.000037 ( 0 hom., cov: 0)
Exomes š: 0.0000017 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KRTAP5-5
NM_001001480.3 missense
NM_001001480.3 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: 1.02
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017537773).
BP6
?
Variant 11-1630415-A-G is Benign according to our data. Variant chr11-1630415-A-G is described in ClinVar as [Benign]. Clinvar id is 403024.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRTAP5-5 | NM_001001480.3 | c.575A>G | p.Tyr192Cys | missense_variant | 1/1 | ENST00000399676.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRTAP5-5 | ENST00000399676.4 | c.575A>G | p.Tyr192Cys | missense_variant | 1/1 | NM_001001480.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 26668Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00535 AC: 204AN: 38148Hom.: 0 AF XY: 0.00658 AC XY: 126AN XY: 19140
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000167 AC: 1AN: 599412Hom.: 0 Cov.: 63 AF XY: 0.00000333 AC XY: 1AN XY: 299886
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000375 AC: 1AN: 26670Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 13096
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Does not pass quality filter - |
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
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
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