rs6733301

Positions:

• chr2-25053415-G-A
• chr2-25053415-G-T

Variant summary

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

The NM_014971.2(EFR3B):​c.7+11096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,140 control chromosomes in the GnomAD database, including 1,311 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 0.12 (1311 hom., cov: 32)
• Consequence: EFR3B NM_014971.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFR3B	NM_014971.2	c.7+11096G>A		intron_variant		ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2	c.-99+10749G>A		intron_variant			NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFR3B	ENST00000403714.8	c.7+11096G>A		intron_variant		5	NM_014971.2	ENSP00000384081	P1
EFR3B	ENST00000401432.7	c.7+11096G>A		intron_variant		2		ENSP00000386082
EFR3B	ENST00000402191.5	c.-99+10749G>A		intron_variant		5		ENSP00000385832

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18865 AN: 152022 Hom.: 1312 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.124 AC: 18879 AN: 152140 Hom.: 1311 Cov.: 32 AF XY: 0.123 AC XY: 9175 AN XY: 74412

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.123

Alfa AF: 0.112 Hom.: 2285

Bravo AF: 0.122

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.46

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: rs6733301; hg19: chr2-25276284;