rs13428823

Variant names:

• chr2-25150429-G-A
• rs13428823
• NM_014971.2:c.2191+687G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 33 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.2191+687G>A		intron_variant	Intron 20 of 22	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.2086+687G>A		intron_variant	Intron 20 of 22		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.2191+687G>A		intron_variant	Intron 20 of 22	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000405108.5	c.1747+687G>A		intron_variant	Intron 17 of 19	1		ENSP00000384454.1
EFR3B	ENST00000402191.5	c.2086+687G>A		intron_variant	Intron 20 of 22	5		ENSP00000385832.1
EFR3B	ENST00000264719.5	c.1696+687G>A		intron_variant	Intron 15 of 17	5		ENSP00000264719.5

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

African (AFR) AF: 0.531 AC: 21967 AN: 41398

American (AMR) AF: 0.531 AC: 8090 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3472

East Asian (EAS) AF: 0.683 AC: 3535 AN: 5176

South Asian (SAS) AF: 0.606 AC: 2917 AN: 4814

European-Finnish (FIN) AF: 0.532 AC: 5579 AN: 10488

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43494 AN: 67964

Other (OTH) AF: 0.627 AC: 1327 AN: 2116

Alfa AF: 0.622 Hom.: 132401

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
PhyloP100		0.79
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13428823; hg19: chr2-25373298;