chr13-106491972-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004093.4(EFNB2):c.*1068C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
EFNB2
NM_004093.4 3_prime_UTR
NM_004093.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.32
Publications
17 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| EFNB2 | NM_004093.4 | c.*1068C>A | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000646441.1 | NP_004084.1 | ||
| EFNB2 | NM_001372056.1 | c.*1068C>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358985.1 | |||
| EFNB2 | NM_001372057.1 | c.*1068C>A | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358986.1 | |||
| EFNB2 | XM_017020406.3 | c.*1068C>A | 3_prime_UTR_variant | Exon 5 of 5 | XP_016875895.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| EFNB2 | ENST00000646441.1 | c.*1068C>A | 3_prime_UTR_variant | Exon 5 of 5 | NM_004093.4 | ENSP00000493716.1 | ||||
| EFNB2 | ENST00000643990.1 | n.1674C>A | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||||
| ENSG00000284966 | ENST00000649449.1 | n.559+267G>T | intron_variant | Intron 1 of 3 | ||||||
| ENSG00000284966 | ENST00000646480.1 | n.-176G>T | upstream_gene_variant |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 460Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 282
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
460
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
282
African (AFR)
AF:
AC:
0
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
430
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
22
Other (OTH)
AF:
AC:
0
AN:
6
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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