chr15-43201879-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP6_ModerateBP7
The NM_001114134.2(EPB42):c.1878G>T(p.Leu626Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L626L) has been classified as Likely benign.
Frequency
Consequence
NM_001114134.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EPB42 | ENST00000441366.7 | c.1878G>T | p.Leu626Leu | synonymous_variant | Exon 12 of 13 | 1 | NM_001114134.2 | ENSP00000396616.2 | ||
ENSG00000285117 | ENST00000563128.5 | n.412G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 3 | ENSP00000520455.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251488Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
Hereditary spherocytosis type 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at