chr15-43203108-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001114134.2(EPB42):c.1779+7A>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 0.000176 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_001114134.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPB42 | ENST00000441366.7 | c.1779+7A>G | splice_region_variant, intron_variant | Intron 11 of 12 | 1 | NM_001114134.2 | ENSP00000396616.2 | |||
ENSG00000285117 | ENST00000563128.5 | n.313+7A>G | splice_region_variant, intron_variant | Intron 2 of 3 | 3 | ENSP00000520455.1 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 152082Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251468Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135904
GnomAD4 exome AF: 0.000181 AC: 264AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.000180 AC XY: 131AN XY: 727196
GnomAD4 genome AF: 0.000131 AC: 20AN: 152200Hom.: 0 Cov.: 31 AF XY: 0.000134 AC XY: 10AN XY: 74422
ClinVar
Submissions by phenotype
Hereditary spherocytosis type 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 06, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at