chr2-25146133-C-T

Variant names:

• chr2-25146133-C-T
• rs1561288
• NM_014971.2:c.2142+1082C>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.2142+1082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 145,872 control chromosomes in the GnomAD database, including 6,692 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 0.29 (6692 hom., cov: 25)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 31 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 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.2142+1082C>T		intron	N/A	NP_055786.1	Q9Y2G0-1
	EFR3B	NM_001319099.2		c.2037+1082C>T		intron	N/A	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.2142+1082C>T		intron	N/A	ENSP00000384081.3	Q9Y2G0-1
	EFR3B	ENST00000405108.5	TSL:1	c.1698+1082C>T		intron	N/A	ENSP00000384454.1	Q9Y2G0-2
	EFR3B	ENST00000401432.7	TSL:2	c.*1037C>T		3_prime_UTR	Exon 19 of 19	ENSP00000386082.3	Q9Y2G0-3

Frequencies

GnomAD3 genomes AF: 0.293 AC: 42728 AN: 145752 Hom.: 6680 Cov.: 25

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.293 AC: 42759 AN: 145860 Hom.: 6692 Cov.: 25 AF XY: 0.303 AC XY: 21359 AN XY: 70412

African (AFR) AF: 0.356 AC: 13973 AN: 39198

American (AMR) AF: 0.385 AC: 5580 AN: 14484

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 718 AN: 3434

East Asian (EAS) AF: 0.309 AC: 1533 AN: 4956

South Asian (SAS) AF: 0.346 AC: 1567 AN: 4530

European-Finnish (FIN) AF: 0.355 AC: 3218 AN: 9068

Middle Eastern (MID) AF: 0.317 AC: 90 AN: 284

European-Non Finnish (NFE) AF: 0.227 AC: 15209 AN: 66988

Other (OTH) AF: 0.264 AC: 535 AN: 2028

Alfa AF: 0.255 Hom.: 12519

Bravo AF: 0.301

Asia WGS AF: 0.332 AC: 1152 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.045
DANN	Benign	0.46
PhyloP100		-2.2
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: rs1561288; hg19: chr2-25369002;