rs4654328
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000347529.7(EPB41):c.-8+16623C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,806 control chromosomes in the GnomAD database, including 8,895 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.31 ( 8895 hom., cov: 30)
Consequence
EPB41
ENST00000347529.7 intron
ENST00000347529.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.426
Genes affected
EPB41 (HGNC:3377): (erythrocyte membrane protein band 4.1) The protein encoded by this gene, together with spectrin and actin, constitute the red cell membrane cytoskeletal network. This complex plays a critical role in erythrocyte shape and deformability. Mutations in this gene are associated with type 1 elliptocytosis (EL1). Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41 | NM_001166005.2 | c.-8+16623C>T | intron_variant | ||||
EPB41 | NM_001166007.2 | c.-618+16623C>T | intron_variant | ||||
EPB41 | NM_001376022.1 | c.-618+16623C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41 | ENST00000347529.7 | c.-8+16623C>T | intron_variant | 1 | |||||
EPB41 | ENST00000373800.7 | c.-698+16623C>T | intron_variant | 1 | |||||
EPB41 | ENST00000373798.5 | c.-8+9996C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.308 AC: 46677AN: 151690Hom.: 8890 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.308 AC: 46697AN: 151806Hom.: 8895 Cov.: 30 AF XY: 0.315 AC XY: 23366AN XY: 74182
GnomAD4 genome
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23366
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74182
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717
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at