rs7589318

Positions:

• chr2-25155503-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.*1163G>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 0.232 in 152,082 control chromosomes in the GnomAD database, including 4,643 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 0.23 (4638 hom., cov: 31)
  • Exomes 𝑓: 0.33 (5 hom.)
• Consequence: EFR3B NM_014971.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774

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 (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.*1163G>A		3_prime_UTR_variant	23/23	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.*1163G>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.*1163G>A		3_prime_UTR_variant	23/23	5	NM_014971.2	ENSP00000384081.3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35247 AN: 151912 Hom.: 4639 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.240

GnomAD4 exome AF: 0.327 AC: 17 AN: 52 Hom.: 5 Cov.: 0 AF XY: 0.294 AC XY: 10 AN XY: 34

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.232 AC: 35252 AN: 152030 Hom.: 4638 Cov.: 31 AF XY: 0.225 AC XY: 16698 AN XY: 74298

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.237

Alfa AF: 0.294 Hom.: 11627

Bravo AF: 0.216

Asia WGS AF: 0.113 AC: 393 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	0.59
DANN	Benign	0.72

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: rs7589318; hg19: chr2-25378372;