rs142447348
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_012156.2(EPB41L1):c.1893C>T(p.Ser631=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00027 ( 0 hom. )
Consequence
EPB41L1
NM_012156.2 synonymous
NM_012156.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.290
Genes affected
EPB41L1 (HGNC:3378): (erythrocyte membrane protein band 4.1 like 1) Erythrocyte membrane protein band 4.1 (EPB41) is a multifunctional protein that mediates interactions between the erythrocyte cytoskeleton and the overlying plasma membrane. The encoded protein binds and stabilizes D2 and D3 dopamine receptors at the neuronal plasma membrane. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 20-36209712-C-T is Benign according to our data. Variant chr20-36209712-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 210948.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.
BP7
?
Synonymous conserved (PhyloP=-0.29 with no splicing effect.
BS2
?
High AC in GnomAd4 at 28 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L1 | NM_012156.2 | c.1893C>T | p.Ser631= | synonymous_variant | 15/22 | ENST00000338074.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L1 | ENST00000338074.7 | c.1893C>T | p.Ser631= | synonymous_variant | 15/22 | 1 | NM_012156.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152184Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000211 AC: 53AN: 251312Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135854
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GnomAD4 exome AF: 0.000266 AC: 389AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.000281 AC XY: 204AN XY: 727234
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GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74488
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | EPB41L1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2018 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 28, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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