chr7-142943600-T-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000420.3(KEL):c.1593-4A>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000526 in 1,607,582 control chromosomes in the GnomAD database, including 5 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_000420.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KEL | NM_000420.3 | c.1593-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000355265.7 | |||
KEL | XM_005249993.2 | c.1629-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
KEL | XM_047420357.1 | c.1482-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KEL | ENST00000355265.7 | c.1593-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000420.3 | P1 | |||
KEL | ENST00000465697.1 | n.454-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 | |||||
KEL | ENST00000470850.1 | n.58-4A>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00287 AC: 436AN: 152090Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000747 AC: 187AN: 250444Hom.: 0 AF XY: 0.000510 AC XY: 69AN XY: 135280
GnomAD4 exome AF: 0.000281 AC: 409AN: 1455374Hom.: 2 Cov.: 32 AF XY: 0.000211 AC XY: 153AN XY: 724504
GnomAD4 genome ? AF: 0.00287 AC: 437AN: 152208Hom.: 3 Cov.: 32 AF XY: 0.00265 AC XY: 197AN XY: 74420
ClinVar
Submissions by phenotype
KEL-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 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