2-25157704-G-A

Position:

• chr2-25157704-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.*3364G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,186 control chromosomes in the GnomAD database, including 37,282 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 0.69 (37255 hom., cov: 31)
  • Exomes 𝑓: 0.64 (27 hom.)
• Consequence: EFR3B NM_014971.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.*3364G>A		3_prime_UTR_variant	23/23	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.*3364G>A		3_prime_UTR_variant	23/23		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.*3364G>A		3_prime_UTR_variant	23/23	5	NM_014971.2	ENSP00000384081	P1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104187 AN: 151926 Hom.: 37189 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.641 AC: 91 AN: 142 Hom.: 27 Cov.: 0 AF XY: 0.625 AC XY: 60 AN XY: 96

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.778

Gnomad4 NFE exome AF: 0.598

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.686 AC: 104300 AN: 152044 Hom.: 37255 Cov.: 31 AF XY: 0.671 AC XY: 49867 AN XY: 74308

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.691

Alfa AF: 0.660 Hom.: 47359

Bravo AF: 0.696

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.51

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: rs1866146; hg19: chr2-25380573;