rs61343376
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001114134.2(EPB42):c.833-4A>G 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 0.00983 in 1,613,598 control chromosomes in the GnomAD database, including 1,101 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_001114134.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB42 | NM_001114134.2 | c.833-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000441366.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB42 | ENST00000441366.7 | c.833-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001114134.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0475 AC: 7215AN: 151944Hom.: 571 Cov.: 32
GnomAD3 exomes AF: 0.0150 AC: 3739AN: 249390Hom.: 244 AF XY: 0.0119 AC XY: 1609AN XY: 135196
GnomAD4 exome AF: 0.00589 AC: 8602AN: 1461536Hom.: 521 Cov.: 32 AF XY: 0.00532 AC XY: 3867AN XY: 727060
GnomAD4 genome ? AF: 0.0477 AC: 7252AN: 152062Hom.: 580 Cov.: 32 AF XY: 0.0450 AC XY: 3346AN XY: 74352
ClinVar
Submissions by phenotype
Hereditary spherocytosis type 5 Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at