17-40818851-A-AGCTGCCGCCGCCGTATCCGCCGCCGGAGCT
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The NM_000421.5(KRT10):c.1654_1683dupAGCTCCGGCGGCGGATACGGCGGCGGCAGC(p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySer) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0897 in 1,344,600 control chromosomes in the GnomAD database, including 10,425 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000421.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT10 | NM_000421.5 | c.1654_1683dupAGCTCCGGCGGCGGATACGGCGGCGGCAGC | p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySer | conservative_inframe_insertion | Exon 7 of 8 | ENST00000269576.6 | NP_000412.4 | |
KRT10 | NM_001379366.1 | c.1654_1683dupAGCTCCGGCGGCGGATACGGCGGCGGCAGC | p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySer | conservative_inframe_insertion | Exon 7 of 8 | NP_001366295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT10 | ENST00000269576.6 | c.1654_1683dupAGCTCCGGCGGCGGATACGGCGGCGGCAGC | p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySer | conservative_inframe_insertion | Exon 7 of 8 | 1 | NM_000421.5 | ENSP00000269576.5 | ||
KRT10 | ENST00000635956.2 | c.1654_1683dupAGCTCCGGCGGCGGATACGGCGGCGGCAGC | p.Ser561_Ser562insSerSerGlyGlyGlyTyrGlyGlyGlySer | conservative_inframe_insertion | Exon 7 of 8 | 2 | ENSP00000490524.2 |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 20235AN: 129164Hom.: 2319 Cov.: 33
GnomAD4 exome AF: 0.0826 AC: 100365AN: 1215346Hom.: 8104 Cov.: 31 AF XY: 0.0829 AC XY: 50199AN XY: 605680
GnomAD4 genome AF: 0.157 AC: 20246AN: 129254Hom.: 2321 Cov.: 33 AF XY: 0.156 AC XY: 9817AN XY: 62940
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
KRT10-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Epidermolytic ichthyosis;C1843463:Annular epidermolytic ichthyosis;C3665704:Congenital reticular ichthyosiform erythroderma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at