chr5-107427427-G-T

Position:

• chr5-107427427-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001962.3(EFNA5):​c.208C>A​(p.Pro70Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EFNA5 NM_001962.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.60

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]

EFNA5 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.812

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFNA5	NM_001962.3	c.208C>A	p.Pro70Thr	missense_variant	2/5	ENST00000333274.11	NP_001953.1
EFNA5	NM_001410773.1	c.208C>A	p.Pro70Thr	missense_variant	2/4		NP_001397702.1
EFNA5	XM_011543250.4	c.154C>A	p.Pro52Thr	missense_variant	2/5		XP_011541552.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFNA5	ENST00000333274.11	c.208C>A	p.Pro70Thr	missense_variant	2/5	1	NM_001962.3	ENSP00000328777.6
EFNA5	ENST00000504941.1	n.480C>A		non_coding_transcript_exon_variant	2/2	1
EFNA5	ENST00000509503.1	c.208C>A	p.Pro70Thr	missense_variant	2/4	5		ENSP00000426989.1
EFNA5	ENST00000505499.1	n.139C>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 30, 2024

The c.208C>A (p.P70T) alteration is located in exon 2 (coding exon 2) of the EFNA5 gene. This alteration results from a C to A substitution at nucleotide position 208, causing the proline (P) at amino acid position 70 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Pathogenic	0.27	D
BayesDel_noAF	Pathogenic	0.16
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T;D;.
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	D;D;D
M_CAP	Benign	0.080	D
MetaRNN	Pathogenic	0.81	D;D;D
MetaSVM	Uncertain	0.42	D
MutationAssessor	Uncertain	2.1	.;M;.
PrimateAI	Pathogenic	0.82	D
PROVEAN	Pathogenic	-5.7	.;D;D
REVEL	Uncertain	0.54
Sift	Uncertain	0.0060	.;D;D
Sift4G	Uncertain	0.017	D;D;D
Polyphen		0.13, 0.48	.;B;P
Vest4		0.74, 0.72
MutPred		0.43		.;Gain of phosphorylation at P70 (P = 0.0377);Gain of phosphorylation at P70 (P = 0.0377);
MVP		0.80
MPC		1.2
ClinPred		0.99	D
GERP RS		6.1
Varity_R		0.74
gMVP		0.67

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-106763128; COSMIC: COSV60949133;