NM_014971.2:c.*120C>A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014971.2(EFR3B):​c.*120C>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 0.0000162 in 923,194 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000046 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000010 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

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.*120C>A		3_prime_UTR	Exon 23 of 23	NP_055786.1
	EFR3B	NM_001319099.2		c.*120C>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.*120C>A		3_prime_UTR	Exon 23 of 23	ENSP00000384081.3
	EFR3B	ENST00000405108.5	TSL:1	c.*120C>A		3_prime_UTR	Exon 20 of 20	ENSP00000384454.1
	EFR3B	ENST00000402191.5	TSL:5	c.*120C>A		3_prime_UTR	Exon 23 of 23	ENSP00000385832.1

Frequencies

GnomAD3 genomes AF: 0.0000461 AC: 7 AN: 151972 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000959

GnomAD4 exome AF: 0.0000104 AC: 8 AN: 771222 Hom.: 0 Cov.: 10 AF XY: 0.0000102 AC XY: 4 AN XY: 392208

African (AFR) AF: 0.00 AC: 0 AN: 18236

American (AMR) AF: 0.000153 AC: 4 AN: 26156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17258

East Asian (EAS) AF: 0.00 AC: 0 AN: 31500

South Asian (SAS) AF: 0.00 AC: 0 AN: 54616

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39670

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3016

European-Non Finnish (NFE) AF: 0.00000367 AC: 2 AN: 544288

Other (OTH) AF: 0.0000548 AC: 2 AN: 36482

GnomAD4 genome AF: 0.0000461 AC: 7 AN: 151972 Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3 AN XY: 74204

African (AFR) AF: 0.00 AC: 0 AN: 41360

American (AMR) AF: 0.000327 AC: 5 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67996

Other (OTH) AF: 0.000959 AC: 2 AN: 2086

Alfa AF: 0.00 Hom.: 7149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		0.58

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;