2-25082887-C-T

Variant names:

• chr2-25082887-C-T
• rs1530016
• NM_014971.2:c.8-8438C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014971.2(EFR3B):​c.8-8438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,028 control chromosomes in the GnomAD database, including 12,133 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 0.36 (12133 hom., cov: 32)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 15 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.8-8438C>T		intron_variant	Intron 1 of 22	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.-98-8438C>T		intron_variant	Intron 1 of 22		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.8-8438C>T		intron_variant	Intron 1 of 22	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000402191.5	c.-98-8438C>T		intron_variant	Intron 1 of 22	5		ENSP00000385832.1
EFR3B	ENST00000401432.7	c.8-8438C>T		intron_variant	Intron 1 of 18	2		ENSP00000386082.3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54825 AN: 151910 Hom.: 12118 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.361 AC: 54842 AN: 152028 Hom.: 12133 Cov.: 32 AF XY: 0.375 AC XY: 27864 AN XY: 74306

African (AFR) AF: 0.106 AC: 4401 AN: 41498

American (AMR) AF: 0.528 AC: 8067 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3472

East Asian (EAS) AF: 0.521 AC: 2692 AN: 5168

South Asian (SAS) AF: 0.437 AC: 2103 AN: 4810

European-Finnish (FIN) AF: 0.581 AC: 6128 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28479 AN: 67942

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.392 Hom.: 26291

Bravo AF: 0.348

Asia WGS AF: 0.496 AC: 1724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.77
PhyloP100		-0.81
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: rs1530016; hg19: chr2-25305756;