chr2-25154460-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.*120C>T		3_prime_UTR_variant	Exon 23 of 23	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.*120C>T		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.*120C>T		3_prime_UTR_variant	Exon 23 of 23	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000405108.5	c.*120C>T		3_prime_UTR_variant	Exon 20 of 20	1		ENSP00000384454.1
EFR3B	ENST00000402191.5	c.*120C>T		3_prime_UTR_variant	Exon 23 of 23	5		ENSP00000385832.1
EFR3B	ENST00000264719.5	c.*120C>T		downstream_gene_variant		5		ENSP00000264719.5

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

Gnomad4 AFR exome AF: 0.327

Gnomad4 AMR exome AF: 0.472

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.652

Gnomad4 SAS exome AF: 0.412

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.273

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

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.286

Alfa AF: 0.236 Hom.: 4517

Bravo AF: 0.315

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.1
DANN	Benign	0.69

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