rs7605927

Positions:

• chr2-25153036-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014971.2(EFR3B):​c.2299-676C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,964 control chromosomes in the GnomAD database, including 9,485 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 0.34 (9485 hom., cov: 32)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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=-0.96).
• 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/exons	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.2299-676C>G		intron_variant		ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.2194-676C>G		intron_variant			NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.2299-676C>G		intron_variant		5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000405108.5	c.1855-676C>G		intron_variant		1		ENSP00000384454.1
EFR3B	ENST00000402191.5	c.2194-676C>G		intron_variant		5		ENSP00000385832.1
EFR3B	ENST00000264719.5	c.1804-676C>G		intron_variant		5		ENSP00000264719.5

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50919 AN: 151846 Hom.: 9463 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.309

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.335 AC: 50970 AN: 151964 Hom.: 9485 Cov.: 32 AF XY: 0.351 AC XY: 26038 AN XY: 74258

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.309

Alfa AF: 0.294 Hom.: 861

Bravo AF: 0.346

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.35

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: rs7605927; hg19: chr2-25375905;