rs7589318

Variant names:

• chr2-25155503-G-A
• rs7589318
• NM_014971.2:c.*1163G>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.*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
• 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=-0.89).
• 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 rank	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.*1163G>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.*1163G>A		3_prime_UTR_variant	Exon 23 of 23		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.*1163G>A		3_prime_UTR_variant	Exon 23 of 23	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000402191.5	c.*1163G>A		downstream_gene_variant		5		ENSP00000385832.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.375 AC: 15 AN: 40

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.130 AC: 5402 AN: 41482

American (AMR) AF: 0.168 AC: 2561 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5184

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4814

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10556

Middle Eastern (MID) AF: 0.240 AC: 69 AN: 288

European-Non Finnish (NFE) AF: 0.316 AC: 21448 AN: 67936

Other (OTH) AF: 0.237 AC: 500 AN: 2112

Alfa AF: 0.286 Hom.: 25866

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
PhyloP100		-0.77

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: rs7589318; hg19: chr2-25378372;