rs9520087
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004093.4(EFNB2):c.*1068C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,416 control chromosomes in the GnomAD database, including 18,656 homozygotes. 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: 𝑓 0.49 ( 18621 hom., cov: 32)
Exomes 𝑓: 0.40 ( 35 hom. )
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFNB2 | NM_004093.4 | c.*1068C>T | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000646441.1 | NP_004084.1 | ||
EFNB2 | NM_001372056.1 | c.*1068C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358985.1 | |||
EFNB2 | NM_001372057.1 | c.*1068C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_001358986.1 | |||
EFNB2 | XM_017020406.3 | c.*1068C>T | 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>T | 3_prime_UTR_variant | Exon 5 of 5 | NM_004093.4 | ENSP00000493716.1 | ||||
EFNB2 | ENST00000643990.1 | n.1674C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | ||||||
ENSG00000284966 | ENST00000649449.1 | n.559+267G>A | intron_variant | Intron 1 of 3 | ||||||
ENSG00000284966 | ENST00000646480.1 | n.-176G>A | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.488 AC: 74092AN: 151838Hom.: 18580 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
74092
AN:
151838
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.396 AC: 182AN: 460Hom.: 35 Cov.: 0 AF XY: 0.397 AC XY: 112AN XY: 282 show subpopulations
GnomAD4 exome
AF:
AC:
182
AN:
460
Hom.:
Cov.:
0
AF XY:
AC XY:
112
AN XY:
282
show subpopulations
African (AFR)
AF:
AC:
1
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:
166
AN:
430
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
11
AN:
22
Other (OTH)
AF:
AC:
4
AN:
6
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.469
Heterozygous variant carriers
0
8
15
23
30
38
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.488 AC: 74191AN: 151956Hom.: 18621 Cov.: 32 AF XY: 0.487 AC XY: 36185AN XY: 74248 show subpopulations
GnomAD4 genome
AF:
AC:
74191
AN:
151956
Hom.:
Cov.:
32
AF XY:
AC XY:
36185
AN XY:
74248
show subpopulations
African (AFR)
AF:
AC:
24521
AN:
41440
American (AMR)
AF:
AC:
7366
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
1560
AN:
3466
East Asian (EAS)
AF:
AC:
3227
AN:
5162
South Asian (SAS)
AF:
AC:
2763
AN:
4816
European-Finnish (FIN)
AF:
AC:
4137
AN:
10534
Middle Eastern (MID)
AF:
AC:
132
AN:
294
European-Non Finnish (NFE)
AF:
AC:
28955
AN:
67948
Other (OTH)
AF:
AC:
1086
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1898
3795
5693
7590
9488
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
670
1340
2010
2680
3350
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2142
AN:
3478
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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