rs375649709
Positions:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS2
The NM_012156.2(EPB41L1):āc.319T>Gā(p.Ser107Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000017 ( 0 hom. )
Consequence
EPB41L1
NM_012156.2 missense
NM_012156.2 missense
Scores
9
7
Clinical Significance
Conservation
PhyloP100: 4.89
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 Likely_benign. Variant got -5 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, EPB41L1
BP6
?
Variant 20-36175692-T-G is Benign according to our data. Variant chr20-36175692-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 129000.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAdExome4 at 25 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L1 | NM_012156.2 | c.319T>G | p.Ser107Ala | missense_variant | 3/22 | ENST00000338074.7 | |
LOC124904892 | XR_007067571.1 | n.405-523A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L1 | ENST00000338074.7 | c.319T>G | p.Ser107Ala | missense_variant | 3/22 | 1 | NM_012156.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727232
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74286
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 14, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D;N;N;N;.;.;N;N;N;N;N
REVEL
Uncertain
Sift
Benign
D;D;D;T;D;.;.;D;D;D;T;D
Sift4G
Benign
T;T;T;D;T;T;T;T;D;T;T;T
Polyphen
B;.;.;B;B;.;B;P;.;.;B;.
Vest4
MVP
MPC
0.84
ClinPred
T
GERP RS
Varity_R
gMVP
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