rs45588736
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_012156.2(EPB41L1):c.1539G>A(p.Glu513Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,614,118 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00045 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00035 ( 2 hom. )
Consequence
EPB41L1
NM_012156.2 synonymous
NM_012156.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.37
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 20-36197912-G-A is Benign according to our data. Variant chr20-36197912-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 210944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.37 with no splicing effect.
BS2
High AC in GnomAd4 at 68 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000358 AC: 90AN: 251462Hom.: 1 AF XY: 0.000338 AC XY: 46AN XY: 135918
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GnomAD4 exome AF: 0.000353 AC: 516AN: 1461888Hom.: 2 Cov.: 32 AF XY: 0.000329 AC XY: 239AN XY: 727244
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GnomAD4 genome AF: 0.000447 AC: 68AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74444
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Nov 28, 2017
Genetic Services Laboratory, University of Chicago
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
not provided Benign:1
Dec 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
EPB41L1: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at