rs1561288

Positions:

• chr2-25146133-C-T

Variant summary

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

The NM_014971.2(EFR3B):​c.2142+1082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 145,872 control chromosomes in the GnomAD database, including 6,692 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 (6692 hom., cov: 25)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

EFR3B (HGNC:29155): (EFR3 homolog B) Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in actin cytoskeleton; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFR3B	NM_014971.2	c.2142+1082C>T		intron_variant		ENST00000403714.8
EFR3B	NM_001319099.2	c.2037+1082C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFR3B	ENST00000403714.8	c.2142+1082C>T		intron_variant		5	NM_014971.2	P1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 42728 AN: 145752 Hom.: 6680 Cov.: 25

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.293 AC: 42759 AN: 145860 Hom.: 6692 Cov.: 25 AF XY: 0.303 AC XY: 21359 AN XY: 70412

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.264

Alfa AF: 0.256 Hom.: 3375

Bravo AF: 0.301

Asia WGS AF: 0.332 AC: 1152 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.045
DANN	Benign	0.46

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: rs1561288; hg19: chr2-25369002;