chr13-106534851-C-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_004093.4(EFNB2):c.114G>T(p.Ser38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,611,432 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 Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
EFNB2
NM_004093.4 synonymous
NM_004093.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0680
Genes affected
EFNB2 (HGNC:3227): (ephrin B2) This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. This gene encodes an EFNB class ephrin which binds to the EPHB4 and EPHA3 receptors. [provided by RefSeq, Jul 2008]
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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=-0.34).
BP6
Variant 13-106534851-C-A is Benign according to our data. Variant chr13-106534851-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3057894.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.068 with no splicing effect.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFNB2 | NM_004093.4 | c.114G>T | p.Ser38= | synonymous_variant | 1/5 | ENST00000646441.1 | |
EFNB2 | NM_001372056.1 | c.114G>T | p.Ser38= | synonymous_variant | 1/4 | ||
EFNB2 | NM_001372057.1 | c.114G>T | p.Ser38= | synonymous_variant | 1/4 | ||
EFNB2 | NM_001372058.1 | c.114G>T | p.Ser38= | synonymous_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFNB2 | ENST00000646441.1 | c.114G>T | p.Ser38= | synonymous_variant | 1/5 | NM_004093.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247502Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134146
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459358Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5AN XY: 725970
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 152074Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74290
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
EFNB2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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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