17-41054896-A-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_033032.3(KRTAP2-2):c.316T>G(p.Ser106Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000074 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KRTAP2-2
NM_033032.3 missense
NM_033032.3 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: -0.900
Publications
0 publications found
Genes affected
KRTAP2-2 (HGNC:18905): (keratin associated protein 2-2) Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.044089794).
BP6
Variant 17-41054896-A-C is Benign according to our data. Variant chr17-41054896-A-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3289684.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_033032.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
0
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000741 AC: 4AN: 539674Hom.: 0 Cov.: 18 AF XY: 0.00000360 AC XY: 1AN XY: 277416 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
539674
Hom.:
Cov.:
18
AF XY:
AC XY:
1
AN XY:
277416
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
6682
American (AMR)
AF:
AC:
0
AN:
20030
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
11594
East Asian (EAS)
AF:
AC:
0
AN:
20984
South Asian (SAS)
AF:
AC:
0
AN:
50878
European-Finnish (FIN)
AF:
AC:
1
AN:
14036
Middle Eastern (MID)
AF:
AC:
0
AN:
1904
European-Non Finnish (NFE)
AF:
AC:
3
AN:
390472
Other (OTH)
AF:
AC:
0
AN:
23094
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
0
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MutPred
Loss of glycosylation at S106 (P = 0.0022)
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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