17-41190230-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001190460.1(KRTAP9-1):​c.344G>C​(p.Cys115Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000801 in 1,248,376 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes š‘“: 8.0e-7 ( 0 hom. )

Consequence

KRTAP9-1
NM_001190460.1 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.218
Variant links:
Genes affected
KRTAP9-1 (HGNC:18912): (keratin associated protein 9-1) 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 Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.32085907).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KRTAP9-1NM_001190460.1 linkc.344G>C p.Cys115Ser missense_variant Exon 1 of 1 ENST00000398470.1 NP_001177389.1 A8MXZ3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KRTAP9-1ENST00000398470.1 linkc.344G>C p.Cys115Ser missense_variant Exon 1 of 1 6 NM_001190460.1 ENSP00000381488.1 A8MXZ3

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
8.01e-7
AC:
1
AN:
1248376
Hom.:
0
Cov.:
134
AF XY:
0.00000162
AC XY:
1
AN XY:
616154
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000155
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.52
CADD
Benign
15
DANN
Benign
0.63
DEOGEN2
Benign
0.061
T;.
Eigen
Benign
-0.36
Eigen_PC
Benign
-0.42
FATHMM_MKL
Benign
0.61
D
LIST_S2
Benign
0.44
T;T
M_CAP
Benign
0.0014
T
MetaRNN
Benign
0.32
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.5
M;.
PrimateAI
Benign
0.25
T
PROVEAN
Uncertain
-4.2
D;.
REVEL
Benign
0.10
Sift
Benign
0.20
T;.
Sift4G
Uncertain
0.027
D;D
Vest4
0.20
MutPred
0.72
Gain of relative solvent accessibility (P = 0.0479);.;
MVP
0.14
MPC
0.032
ClinPred
0.27
T
GERP RS
1.5
Varity_R
0.15
gMVP
0.099

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-39346482; API