2-25154460-C-T

Variant names:

• chr2-25154460-C-T
• rs2118404
• NM_014971.2:c.*120C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014971.2(EFR3B):​c.*120C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 921,526 control chromosomes in the GnomAD database, including 40,933 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 0.31 (7947 hom., cov: 32)
  • Exomes 𝑓: 0.27 (32986 hom.)
• Consequence: EFR3B NM_014971.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 13 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	NM_014971.2	MANE Select	c.*120C>T		3_prime_UTR	Exon 23 of 23	NP_055786.1	Q9Y2G0-1
	EFR3B	NM_001319099.2		c.*120C>T		3_prime_UTR	Exon 23 of 23	NP_001306028.1	E7ESK9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	ENST00000403714.8	TSL:5 MANE Select	c.*120C>T		3_prime_UTR	Exon 23 of 23	ENSP00000384081.3	Q9Y2G0-1
	EFR3B	ENST00000405108.5	TSL:1	c.*120C>T		3_prime_UTR	Exon 20 of 20	ENSP00000384454.1	Q9Y2G0-2
	EFR3B	ENST00000858650.1		c.*120C>T		3_prime_UTR	Exon 23 of 23	ENSP00000528709.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46832 AN: 151896 Hom.: 7934 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.266 AC: 204449 AN: 769512 Hom.: 32986 Cov.: 10 AF XY: 0.270 AC XY: 105625 AN XY: 391354

African (AFR) AF: 0.327 AC: 5952 AN: 18198

American (AMR) AF: 0.472 AC: 12313 AN: 26088

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 3489 AN: 17238

East Asian (EAS) AF: 0.652 AC: 20523 AN: 31458

South Asian (SAS) AF: 0.412 AC: 22464 AN: 54486

European-Finnish (FIN) AF: 0.357 AC: 14154 AN: 39598

Middle Eastern (MID) AF: 0.294 AC: 887 AN: 3014

European-Non Finnish (NFE) AF: 0.211 AC: 114713 AN: 542990

Other (OTH) AF: 0.273 AC: 9954 AN: 36442

GnomAD4 genome AF: 0.308 AC: 46855 AN: 152014 Hom.: 7947 Cov.: 32 AF XY: 0.324 AC XY: 24050 AN XY: 74298

African (AFR) AF: 0.335 AC: 13884 AN: 41452

American (AMR) AF: 0.405 AC: 6186 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3100 AN: 5152

South Asian (SAS) AF: 0.441 AC: 2123 AN: 4812

European-Finnish (FIN) AF: 0.391 AC: 4137 AN: 10568

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15659 AN: 67974

Other (OTH) AF: 0.286 AC: 603 AN: 2108

Alfa AF: 0.247 Hom.: 7149

Bravo AF: 0.315

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

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: rs2118404; hg19: chr2-25377329; COSMIC: COSV53123354; COSMIC: COSV53123354;