NM_001962.3:c.126-41153T>C

Variant names:

• chr5-107468662-A-G
• rs26247
• NM_001962.3:c.126-41153T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001962.3(EFNA5):​c.126-41153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,102 control chromosomes in the GnomAD database, including 7,459 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 0.29 (7459 hom., cov: 33)
• Consequence: EFNA5 NM_001962.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFNA5	NM_001962.3	c.126-41153T>C		intron_variant	Intron 1 of 4	ENST00000333274.11	NP_001953.1
EFNA5	NM_001410773.1	c.126-41153T>C		intron_variant	Intron 1 of 3		NP_001397702.1
EFNA5	XM_011543250.4	c.71+25241T>C		intron_variant	Intron 1 of 4		XP_011541552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFNA5	ENST00000333274.11	c.126-41153T>C		intron_variant	Intron 1 of 4	1	NM_001962.3	ENSP00000328777.6
EFNA5	ENST00000504941.1	n.398-41153T>C		intron_variant	Intron 1 of 1	1
EFNA5	ENST00000509503.1	c.126-41153T>C		intron_variant	Intron 1 of 3	5		ENSP00000426989.1
EFNA5	ENST00000505499.1	n.56+37474T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43622 AN: 151984 Hom.: 7457 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.287 AC: 43657 AN: 152102 Hom.: 7459 Cov.: 33 AF XY: 0.300 AC XY: 22274 AN XY: 74338

African (AFR) AF: 0.325 AC: 13471 AN: 41488

American (AMR) AF: 0.401 AC: 6115 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 585 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3490 AN: 5160

South Asian (SAS) AF: 0.517 AC: 2496 AN: 4830

European-Finnish (FIN) AF: 0.336 AC: 3558 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13232 AN: 67992

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.218 Hom.: 6527

Bravo AF: 0.293

Asia WGS AF: 0.554 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.36
DANN	Benign	0.67
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs26247; hg19: chr5-106804363;