rs13428823

chr2-25150429-G-A

Variant summary

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

The NM_014971.2(EFR3B):c.2191+687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,864 control chromosomes in the GnomAD database, including 26,854 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 0.59 (26854 hom., cov: 31)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.790

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFR3B	NM_014971.2	c.2191+687G>A		intron_variant		ENST00000403714.8
EFR3B	NM_001319099.2	c.2086+687G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFR3B	ENST00000403714.8	c.2191+687G>A		intron_variant		5	NM_014971.2	P1
EFR3B	ENST00000405108.5	c.1747+687G>A		intron_variant		1
EFR3B	ENST00000264719.5	c.1696+687G>A		intron_variant		5
EFR3B	ENST00000402191.5	c.2086+687G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89680 AN: 151746 Hom.: 26835 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.591 AC: 89740 AN: 151864 Hom.: 26854 Cov.: 31 AF XY: 0.584 AC XY: 43315 AN XY: 74206

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.627

Alfa AF: 0.628 Hom.: 61574

Bravo AF: 0.586

Asia WGS AF: 0.631 AC: 2192 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.6
Dann	Benign	0.40

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: rs13428823; hg19: chr2-25373298;