2-25154460-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014971.2(EFR3B):​c.*120C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 10

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.63

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;