rs10043302

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001962.3(EFNA5):​c.125+96692C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,136 control chromosomes in the GnomAD database, including 1,914 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 0.13 ( 1914 hom., cov: 32)

Consequence

EFNA5
NM_001962.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00300
Variant links:
Genes affected
EFNA5 (HGNC:3225): (ephrin A5) Ephrin-A5, a member of the ephrin gene family, prevents axon bundling in cocultures of cortical neurons with astrocytes, a model of late stage nervous system development and differentiation. The EPH and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, particularly in the nervous system. EPH receptors typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin ligands and receptors have been named by the Eph Nomenclature Committee (1997). 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. The Eph family of receptors are similarly divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EFNA5NM_001962.3 linkuse as main transcriptc.125+96692C>G intron_variant ENST00000333274.11
EFNA5NM_001410773.1 linkuse as main transcriptc.125+96692C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EFNA5ENST00000333274.11 linkuse as main transcriptc.125+96692C>G intron_variant 1 NM_001962.3 P3
EFNA5ENST00000504941.1 linkuse as main transcriptn.397+96692C>G intron_variant, non_coding_transcript_variant 1
EFNA5ENST00000509503.1 linkuse as main transcriptc.125+96692C>G intron_variant 5 A1

Frequencies

GnomAD3 genomes
AF:
0.131
AC:
19859
AN:
152018
Hom.:
1914
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.272
Gnomad AMI
AF:
0.207
Gnomad AMR
AF:
0.0766
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.00772
Gnomad SAS
AF:
0.0381
Gnomad FIN
AF:
0.0808
Gnomad MID
AF:
0.0823
Gnomad NFE
AF:
0.0817
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.131
AC:
19878
AN:
152136
Hom.:
1914
Cov.:
32
AF XY:
0.128
AC XY:
9532
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.271
Gnomad4 AMR
AF:
0.0765
Gnomad4 ASJ
AF:
0.110
Gnomad4 EAS
AF:
0.00774
Gnomad4 SAS
AF:
0.0377
Gnomad4 FIN
AF:
0.0808
Gnomad4 NFE
AF:
0.0817
Gnomad4 OTH
AF:
0.109
Alfa
AF:
0.114
Hom.:
177
Bravo
AF:
0.139
Asia WGS
AF:
0.0340
AC:
119
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.0
DANN
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10043302; hg19: chr5-106909498; API