chr17-40818851-A-AGCT
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_000421.5(KRT10):c.1681_1683dupAGC(p.Ser561dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000619 in 1,406,058 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000421.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT10 | NM_000421.5 | c.1681_1683dupAGC | p.Ser561dup | conservative_inframe_insertion | Exon 7 of 8 | ENST00000269576.6 | NP_000412.4 | |
KRT10 | NM_001379366.1 | c.1681_1683dupAGC | p.Ser561dup | 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.1681_1683dupAGC | p.Ser561dup | conservative_inframe_insertion | Exon 7 of 8 | 1 | NM_000421.5 | ENSP00000269576.5 | ||
KRT10 | ENST00000635956.2 | c.1681_1683dupAGC | p.Ser561dup | conservative_inframe_insertion | Exon 7 of 8 | 2 | ENSP00000490524.2 |
Frequencies
GnomAD3 genomes AF: 0.000306 AC: 40AN: 130756Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000369 AC: 47AN: 1275200Hom.: 0 Cov.: 31 AF XY: 0.0000300 AC XY: 19AN XY: 634360
GnomAD4 genome AF: 0.000306 AC: 40AN: 130858Hom.: 0 Cov.: 33 AF XY: 0.000314 AC XY: 20AN XY: 63688
ClinVar
Submissions by phenotype
not provided Uncertain:3
This variant, c.1681_1683dup, results in the insertion of 1 amino acid(s) of the KRT10 protein (p.Ser563dup), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KRT10-related conditions. ClinVar contains an entry for this variant (Variation ID: 1319423). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Has not been previously published as pathogenic or benign to our knowledge; In-frame deletion of 1 amino acid in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at