chr5-107615656-G-A

Position:

• chr5-107615656-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001962.3(EFNA5):​c.125+54833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,060 control chromosomes in the GnomAD database, including 2,957 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 0.17 (2957 hom., cov: 32)
• Consequence: EFNA5 NM_001962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFNA5	NM_001962.3	c.125+54833C>T		intron_variant		ENST00000333274.11
EFNA5	NM_001410773.1	c.125+54833C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFNA5	ENST00000333274.11	c.125+54833C>T		intron_variant		1	NM_001962.3	P3
EFNA5	ENST00000504941.1	n.397+54833C>T		intron_variant, non_coding_transcript_variant		1
EFNA5	ENST00000509503.1	c.125+54833C>T		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26142 AN: 151942 Hom.: 2958 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.203

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.172 AC: 26144 AN: 152060 Hom.: 2957 Cov.: 32 AF XY: 0.176 AC XY: 13104 AN XY: 74348

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.203

Alfa AF: 0.208 Hom.: 4744

Bravo AF: 0.163

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs17160255; hg19: chr5-106951357;