3-134795684-T-C

Variant names:

• chr3-134795684-T-C
• rs1428579099
• NM_004441.5:c.53T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004441.5(EPHB1):​c.53T>C​(p.Met18Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M18V) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: EPHB1 NM_004441.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.53

Genes affected

EPHB1 (HGNC:3392): (EPH receptor B1) Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. 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 divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The protein encoded by this gene is a receptor for ephrin-B family members. [provided by RefSeq, Jul 2008]

ENSG00000288700 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14053988).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EPHB1	NM_004441.5	c.53T>C	p.Met18Thr	missense_variant	Exon 1 of 16	ENST00000398015.8	NP_004432.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EPHB1	ENST00000398015.8	c.53T>C	p.Met18Thr	missense_variant	Exon 1 of 16	1	NM_004441.5	ENSP00000381097.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457728 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 725274

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 32558

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 44540

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 25934

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39186

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 85848

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 53292

Gnomad4 NFE exome AF: 0.00 AC: 0 AN: 1110396

Gnomad4 Remaining exome AF: 0.0000166 AC: 1 AN: 60226

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 27, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.53T>C (p.M18T) alteration is located in exon 1 (coding exon 1) of the EPHB1 gene. This alteration results from a T to C substitution at nucleotide position 53, causing the methionine (M) at amino acid position 18 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	0.083
BayesDel_addAF	Benign	-0.035	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	21
DANN	Benign	0.86
DEOGEN2	Benign	0.066	T;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.16
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.65	T;T
M_CAP	Uncertain	0.14	D
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.20	N;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-0.31	N;.
REVEL	Benign	0.16
Sift	Benign	0.42	T;.
Sift4G	Benign	0.57	T;.
Polyphen		0.0	B;.
Vest4		0.37
MutPred		0.45		Loss of helix (P = 0.0104);Loss of helix (P = 0.0104);
MVP		0.69
MPC		0.52
ClinPred		0.17	T
GERP RS		4.5
Varity_R		0.19
gMVP		0.40
Mutation Taster		=65/35	polymorphism

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: rs1428579099; hg19: chr3-134514526;