2-25078886-A-T

Position:

• chr2-25078886-A-T

Variant summary

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

The NM_014971.2(EFR3B):​c.8-12439A>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 151,968 control chromosomes in the GnomAD database, including 12,173 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 (12173 hom., cov: 31)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760

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=-0.89).
• 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/exons	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.8-12439A>T		intron_variant		ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.-98-12439A>T		intron_variant			NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.8-12439A>T		intron_variant		5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000402191.5	c.-98-12439A>T		intron_variant		5		ENSP00000385832.1
EFR3B	ENST00000401432.7	c.8-12439A>T		intron_variant		2		ENSP00000386082.3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54883 AN: 151848 Hom.: 12158 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.361 AC: 54900 AN: 151968 Hom.: 12173 Cov.: 31 AF XY: 0.376 AC XY: 27884 AN XY: 74252

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.391

Alfa AF: 0.393 Hom.: 1682

Bravo AF: 0.349

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.75

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: rs478222; hg19: chr2-25301755;