chr13-106500643-G-C

Position:

• chr13-106500643-G-C

Variant summary

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

The NM_004093.4(EFNB2):​c.407-4803C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,154 control chromosomes in the GnomAD database, including 54,420 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 0.84 (54420 hom., cov: 31)
• Consequence: EFNB2 NM_004093.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

EFNB2 (HGNC:3227): (ephrin B2) This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. 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. This gene encodes an EFNB class ephrin which binds to the EPHB4 and EPHA3 receptors. [provided by RefSeq, Jul 2008]

ENSG00000284966 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFNB2	NM_004093.4	c.407-4803C>G		intron_variant		ENST00000646441.1	NP_004084.1
EFNB2	NM_001372056.1	c.407-5649C>G		intron_variant			NP_001358985.1
EFNB2	NM_001372057.1	c.407-4803C>G		intron_variant			NP_001358986.1
EFNB2	XM_017020406.3	c.413-4803C>G		intron_variant			XP_016875895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFNB2	ENST00000646441.1	c.407-4803C>G		intron_variant			NM_004093.4	ENSP00000493716.1
ENSG00000284966	ENST00000642447.1	n.85+7765G>C		intron_variant
EFNB2	ENST00000643990.1	n.11-4803C>G		intron_variant
ENSG00000284966	ENST00000646480.1	n.496+7765G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128042 AN: 152034 Hom.: 54377 Cov.: 31

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.842 AC: 128139 AN: 152154 Hom.: 54420 Cov.: 31 AF XY: 0.847 AC XY: 62974 AN XY: 74372

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.855

Alfa AF: 0.858 Hom.: 6597

Bravo AF: 0.839

Asia WGS AF: 0.931 AC: 3237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9301141; hg19: chr13-107152991;