chr17-41620565-G-GA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000422.3(KRT17):c.1182-8_1182-7insT 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 0.0147 in 145,326 control chromosomes in the GnomAD database, including 28 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 28 hom., cov: 31)
Exomes 𝑓: 0.085 ( 45 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 Benign. Variant got -10 ACMG points.
BP6
?
Variant 17-41620565-G-GA is Benign according to our data. Variant chr17-41620565-G-GA is described in ClinVar as [Benign]. Clinvar id is 1528628.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (2140/145326) while in subpopulation NFE AF= 0.0195 (1281/65662). AF 95% confidence interval is 0.0186. There are 28 homozygotes in gnomad4. There are 961 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2139 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT17 | NM_000422.3 | c.1182-8_1182-7insT | 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_1182-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000422.3 | P1 | |||
KRT17 | ENST00000648859.1 | c.172-8_172-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||||
KRT17 | ENST00000493253.5 | n.1569-8_1569-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
KRT17 | ENST00000649249.1 | n.458-8_458-7insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0147 AC: 2139AN: 145248Hom.: 28 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.0852 AC: 62484AN: 732962Hom.: 45 Cov.: 36 AF XY: 0.0839 AC XY: 30025AN XY: 357924
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Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
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GnomAD4 genome ? AF: 0.0147 AC: 2140AN: 145326Hom.: 28 Cov.: 31 AF XY: 0.0136 AC XY: 961AN XY: 70470
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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 | Jan 20, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at