2-25157704-G-A

Variant names:

• chr2-25157704-G-A
• rs1866146
• NM_014971.2:c.*3364G>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.*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
• Publications: 33 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014971.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	NM_014971.2	MANE Select	c.*3364G>A		3_prime_UTR	Exon 23 of 23	NP_055786.1
	EFR3B	NM_001319099.2		c.*3364G>A		3_prime_UTR	Exon 23 of 23	NP_001306028.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	ENST00000403714.8	TSL:5 MANE Select	c.*3364G>A		3_prime_UTR	Exon 23 of 23	ENSP00000384081.3

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.778 AC: 28 AN: 36

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.598 AC: 55 AN: 92

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.878 AC: 36443 AN: 41500

American (AMR) AF: 0.553 AC: 8433 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2055 AN: 5172

South Asian (SAS) AF: 0.547 AC: 2629 AN: 4810

European-Finnish (FIN) AF: 0.500 AC: 5280 AN: 10568

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44938 AN: 67946

Other (OTH) AF: 0.691 AC: 1462 AN: 2116

Alfa AF: 0.667 Hom.: 72632

Bravo AF: 0.696

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		0.39

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: rs1866146; hg19: chr2-25380573;