17-41501359-C-CT
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_153490.3(KRT13):c.1273dupA(p.Ser425LysfsTer6) variant causes a frameshift, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,558,802 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S425S) has been classified as Uncertain significance.
Frequency
Consequence
NM_153490.3 frameshift, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT13 | NM_153490.3 | c.1273dupA | p.Ser425LysfsTer6 | frameshift_variant, splice_region_variant | Exon 8 of 8 | ENST00000246635.8 | NP_705694.3 | |
KRT13 | NM_002274.4 | c.1247dupA | p.Arg417AlafsTer82 | frameshift_variant, splice_region_variant | Exon 7 of 7 | NP_002265.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000468 AC: 78AN: 166640Hom.: 0 AF XY: 0.000513 AC XY: 45AN XY: 87684
GnomAD4 exome AF: 0.000122 AC: 171AN: 1406518Hom.: 0 Cov.: 30 AF XY: 0.000135 AC XY: 94AN XY: 694370
GnomAD4 genome AF: 0.000131 AC: 20AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at