2-25053415-G-A

Variant names:

• chr2-25053415-G-A
• rs6733301
• NM_014971.2:c.7+11096G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	NM_014971.2	MANE Select	c.7+11096G>A		intron	N/A	NP_055786.1
	EFR3B	NM_001319099.2		c.-99+10749G>A		intron	N/A	NP_001306028.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFR3B	ENST00000403714.8	TSL:5 MANE Select	c.7+11096G>A		intron	N/A	ENSP00000384081.3
	EFR3B	ENST00000402191.5	TSL:5	c.-99+10749G>A		intron	N/A	ENSP00000385832.1
	EFR3B	ENST00000401432.7	TSL:2	c.7+11096G>A		intron	N/A	ENSP00000386082.3

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

African (AFR) AF: 0.168 AC: 6958 AN: 41496

American (AMR) AF: 0.0774 AC: 1183 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5176

South Asian (SAS) AF: 0.197 AC: 946 AN: 4814

European-Finnish (FIN) AF: 0.105 AC: 1117 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7892 AN: 67988

Other (OTH) AF: 0.123 AC: 260 AN: 2116

Alfa AF: 0.116 Hom.: 3508

Bravo AF: 0.122

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		-0.15
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: rs6733301; hg19: chr2-25276284;