Genetic Variant EFR3B:c.212+46T>C (chr2-25093176-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014971.2(EFR3B):c.212+46T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 1,544,070 control chromosomes in the GnomAD database, including 5,027 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 0.11 ( 2373 hom., cov: 32)

Exomes 𝑓: 0.037 ( 2654 hom. )

Consequence

EFR3B
NM_014971.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.604

Publications

8 publications found

Variant links:

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]

EFR3B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFR3B	NM_014971.2 link	c.212+46T>C		intron_variant	Intron 3 of 22	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2 link	c.107+46T>C		intron_variant	Intron 3 of 22		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
EFR3B	ENST00000403714.8 link	c.212+46T>C	intron_variant	Intron 3 of 22	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000402191.5 link	c.107+46T>C	intron_variant	Intron 3 of 22	5		ENSP00000385832.1
EFR3B	ENST00000401432.7 link	c.212+46T>C	intron_variant	Intron 3 of 18	2		ENSP00000386082.3

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17079

AN:

152018

Hom.:

2365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.0463

Gnomad ASJ

AF:

0.0410

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0564

Gnomad FIN

AF:

0.0131

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0271

Gnomad OTH

AF:

0.0833

GnomAD2 exomes

AF:

0.0475

AC:

7355

AN:

154774

AF XY:

0.0452

show subpopulations

Gnomad AFR exome

AF:

0.351

Gnomad AMR exome

AF:

0.0262

Gnomad ASJ exome

AF:

0.0472

Gnomad EAS exome

AF:

0.000461

Gnomad FIN exome

AF:

0.0167

Gnomad NFE exome

AF:

0.0285

Gnomad OTH exome

AF:

0.0395

GnomAD4 exome

AF:

0.0372

AC:

51748

AN:

1391934

Hom.:

2654

Cov.:

AF XY:

0.0369

AC XY:

25328

AN XY:

685742

show subpopulations

African (AFR)

AF:

0.347

AC:

10869

AN:

31344

American (AMR)

AF:

0.0304

AC:

1068

AN:

35178

Ashkenazi Jewish (ASJ)

AF:

0.0462

AC:

1154

AN:

24954

East Asian (EAS)

AF:

0.000337

AC:

AN:

35612

South Asian (SAS)

AF:

0.0560

AC:

4411

AN:

78790

European-Finnish (FIN)

AF:

0.0161

AC:

771

AN:

47816

Middle Eastern (MID)

AF:

0.0548

AC:

311

AN:

5680

European-Non Finnish (NFE)

AF:

0.0282

AC:

30269

AN:

1074756

Other (OTH)

AF:

0.0499

AC:

2883

AN:

57804

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

2114

4228

6343

8457

10571

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1350

2700

4050

5400

6750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.112

AC:

17102

AN:

152136

Hom.:

2373

Cov.:

AF XY:

0.108

AC XY:

8072

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.331

AC:

13716

AN:

41440

American (AMR)

AF:

0.0462

AC:

707

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0410

AC:

142

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5168

South Asian (SAS)

AF:

0.0570

AC:

275

AN:

4822

European-Finnish (FIN)

AF:

0.0131

AC:

139

AN:

10610

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0271

AC:

1845

AN:

68020

Other (OTH)

AF:

0.0833

AC:

176

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

619

1238

1858

2477

3096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0572

Hom.:

2576

Bravo

AF:

0.126

Asia WGS

AF:

0.0570

AC:

199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.5

(source)

DANN

Benign

0.52

PhyloP100

0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over