17-40818497-G-GA
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_000421.5(KRT10):c.1749-16dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000386 in 1,553,706 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000036 ( 0 hom. )
Consequence
KRT10
NM_000421.5 intron
NM_000421.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.512
Genes affected
KRT10 (HGNC:6413): (keratin 10) This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
Variant 17-40818497-G-GA is Benign according to our data. Variant chr17-40818497-G-GA is described in ClinVar as [Benign]. Clinvar id is 2787839.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT10 | NM_000421.5 | c.1749-16dupT | intron_variant | ENST00000269576.6 | NP_000412.4 | |||
KRT10 | NM_001379366.1 | c.1769-16dupT | intron_variant | NP_001366295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT10 | ENST00000269576.6 | c.1749-16dupT | intron_variant | 1 | NM_000421.5 | ENSP00000269576.5 | ||||
KRT10 | ENST00000635956.2 | c.1769-16dupT | intron_variant | 2 | ENSP00000490524.2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151768Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000357 AC: 5AN: 1401938Hom.: 0 Cov.: 23 AF XY: 0.00000428 AC XY: 3AN XY: 701188
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151768Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74088
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Aug 03, 2023 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at