rs688969

chrX-68841388-A-CchrX-68841388-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004429.5(EFNB1):c.*734A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.61 (15197 hom., 18119 hem., cov: 22)
  • Exomes 𝑓: 0.61 (40 hom. 99 hem.)
  • Failed GnomAD Quality Control
• Consequence: EFNB1 NM_004429.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

EFNB1 (HGNC:3226): (ephrin B1) The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd at 15201 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFNB1	NM_004429.5	c.*734A>C		3_prime_UTR_variant	5/5	ENST00000204961.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFNB1	ENST00000204961.5	c.*734A>C		3_prime_UTR_variant	5/5	1	NM_004429.5	P1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 66121 AN: 108461 Hom.: 15201 Cov.: 22 AF XY: 0.580 AC XY: 18091 AN XY: 31217

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.624

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.610 AC: 225 AN: 369 Hom.: 40 Cov.: 0 AF XY: 0.631 AC XY: 99 AN XY: 157

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.560

Gnomad4 NFE exome AF: 0.821

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.610 AC: 66140 AN: 108506 Hom.: 15197 Cov.: 22 AF XY: 0.579 AC XY: 18119 AN XY: 31274

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.617

Alfa AF: 0.562 Hom.: 3176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.0
Dann	Benign	0.47

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: rs688969; hg19: chrX-68061231; COSMIC: COSV52662638;