chr17-41620565-G-GAA
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000422.3(KRT17):c.1182-8_1182-7insTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 145,366 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000069 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00010 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KRT17
NM_000422.3 splice_region, splice_polypyrimidine_tract, intron
NM_000422.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.262
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 17-41620565-G-GAA is Benign according to our data. Variant chr17-41620565-G-GAA is described in ClinVar as [Likely_benign]. Clinvar id is 3037508.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT17 | NM_000422.3 | c.1182-8_1182-7insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000311208.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT17 | ENST00000311208.13 | c.1182-8_1182-7insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000422.3 | P1 | |||
KRT17 | ENST00000648859.1 | c.172-8_172-7insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||||
KRT17 | ENST00000493253.5 | n.1569-8_1569-7insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
KRT17 | ENST00000649249.1 | n.458-8_458-7insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000688 AC: 1AN: 145366Hom.: 0 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000101 AC: 118AN: 1164332Hom.: 0 Cov.: 36 AF XY: 0.000103 AC XY: 60AN XY: 581222
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GnomAD4 genome ? AF: 0.00000688 AC: 1AN: 145366Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 70450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
KRT17-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at