17-41620795-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000422.3(KRT17):c.1045G>A(p.Val349Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000361 in 1,613,122 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00062 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 6 hom. )
Consequence
KRT17
NM_000422.3 missense
NM_000422.3 missense
Scores
2
11
Clinical Significance
Conservation
PhyloP100: 0.160
Genes affected
KRT17 (HGNC:6427): (keratin 17) This gene encodes the type I intermediate filament chain keratin 17, expressed in nail bed, hair follicle, sebaceous glands, and other epidermal appendages. Mutations in this gene lead to Jackson-Lawler type pachyonychia congenita and steatocystoma multiplex. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009829462).
BP6
?
Variant 17-41620795-C-T is Benign according to our data. Variant chr17-41620795-C-T is described in ClinVar as [Benign]. Clinvar id is 1581086.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000624 (95/152344) while in subpopulation EAS AF= 0.016 (83/5188). AF 95% confidence interval is 0.0132. There are 1 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 95 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT17 | NM_000422.3 | c.1045G>A | p.Val349Met | missense_variant | 6/8 | ENST00000311208.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT17 | ENST00000311208.13 | c.1045G>A | p.Val349Met | missense_variant | 6/8 | 1 | NM_000422.3 | P1 | |
KRT17 | ENST00000648859.1 | c.37G>A | p.Val13Met | missense_variant | 1/2 | ||||
KRT17 | ENST00000493253.5 | n.1432G>A | non_coding_transcript_exon_variant | 5/7 | 2 | ||||
KRT17 | ENST00000649249.1 | n.321G>A | non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes ? AF: 0.000624 AC: 95AN: 152226Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00120 AC: 302AN: 250894Hom.: 3 AF XY: 0.00120 AC XY: 163AN XY: 135680
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GnomAD4 exome AF: 0.000333 AC: 487AN: 1460778Hom.: 6 Cov.: 36 AF XY: 0.000329 AC XY: 239AN XY: 726718
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
D;D;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
N;D
PrimateAI
Benign
T
Polyphen
B;B;.
Vest4
0.37, 0.44
MVP
0.87
MPC
0.44
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