chr17-41501711-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153490.3(KRT13):c.1270+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000978 in 1,583,804 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_153490.3 splice_region, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT13 | NM_153490.3 | c.1270+8A>G | splice_region_variant, intron_variant | ENST00000246635.8 | |||
KRT13 | NM_002274.4 | c.1245-349A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT13 | ENST00000246635.8 | c.1270+8A>G | splice_region_variant, intron_variant | 1 | NM_153490.3 | P2 | |||
ENST00000411759.1 | n.334+395T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 87AN: 152100Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00235 AC: 479AN: 204206Hom.: 11 AF XY: 0.00301 AC XY: 328AN XY: 109030
GnomAD4 exome AF: 0.00102 AC: 1463AN: 1431586Hom.: 29 Cov.: 33 AF XY: 0.00145 AC XY: 1030AN XY: 708848
GnomAD4 genome ? AF: 0.000565 AC: 86AN: 152218Hom.: 1 Cov.: 33 AF XY: 0.000860 AC XY: 64AN XY: 74410
ClinVar
Submissions by phenotype
KRT13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at