chr5-112195690-A-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022140.5(EPB41L4A):c.1395T>A(p.Gly465=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00822 in 1,613,490 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0058 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 57 hom. )
Consequence
EPB41L4A
NM_022140.5 synonymous
NM_022140.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00600
Genes affected
EPB41L4A (HGNC:13278): (erythrocyte membrane protein band 4.1 like 4A) The protein encoded by this gene is a member of the band 4.1 protein superfamily. Members of this superfamily are thought to play an important role in regulating interactions between the cytoskeleton and plasma membrane, and contain an amino terminal conserved domain that binds glycophorin C. This gene product is thought to be involved in the beta-catenin signaling pathway. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 5-112195690-A-T is Benign according to our data. Variant chr5-112195690-A-T is described in ClinVar as [Benign]. Clinvar id is 714299.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.006 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L4A | NM_022140.5 | c.1395T>A | p.Gly465= | synonymous_variant | 16/23 | ENST00000261486.6 | |
LOC124901044 | XR_007058902.1 | n.63+1031A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L4A | ENST00000261486.6 | c.1395T>A | p.Gly465= | synonymous_variant | 16/23 | 1 | NM_022140.5 | P1 | |
ENST00000506875.1 | n.96+1031A>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00581 AC: 883AN: 152066Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00572 AC: 1425AN: 249088Hom.: 3 AF XY: 0.00558 AC XY: 754AN XY: 135144
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GnomAD4 exome AF: 0.00847 AC: 12384AN: 1461306Hom.: 57 Cov.: 30 AF XY: 0.00821 AC XY: 5968AN XY: 726964
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GnomAD4 genome ? AF: 0.00580 AC: 883AN: 152184Hom.: 1 Cov.: 32 AF XY: 0.00528 AC XY: 393AN XY: 74420
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at