Genetic Variant EFR3B:c.*120C>T (chr2-25154460-C-T) – 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.*120C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 921,526 control chromosomes in the GnomAD database, including 40,933 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 0.31 ( 7947 hom., cov: 32)

Exomes 𝑓: 0.27 ( 32986 hom. )

Consequence

EFR3B
NM_014971.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.577

Publications

13 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:

Genome browser will be placed here

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=-0.79).

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 rank	MANE	Protein	UniProt
EFR3B	NM_014971.2 link	c.*120C>T		3_prime_UTR_variant	Exon 23 of 23	ENST00000403714.8	NP_055786.1
EFR3B	NM_001319099.2 link	c.*120C>T		3_prime_UTR_variant	Exon 23 of 23		NP_001306028.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
EFR3B	ENST00000403714.8 link	c.*120C>T	3_prime_UTR_variant	Exon 23 of 23	5	NM_014971.2	ENSP00000384081.3
EFR3B	ENST00000405108.5 link	c.*120C>T	3_prime_UTR_variant	Exon 20 of 20	1		ENSP00000384454.1
EFR3B	ENST00000402191.5 link	c.*120C>T	3_prime_UTR_variant	Exon 23 of 23	5		ENSP00000385832.1
EFR3B	ENST00000264719.5 link	c.*120C>T	downstream_gene_variant		5		ENSP00000264719.5

Frequencies

GnomAD3 genomes

AF:

0.308

AC:

46832

AN:

151896

Hom.:

7934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.602

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.286

GnomAD4 exome

AF:

0.266

AC:

204449

AN:

769512

Hom.:

32986

Cov.:

AF XY:

0.270

AC XY:

105625

AN XY:

391354

show subpopulations

African (AFR)

AF:

0.327

AC:

5952

AN:

18198

American (AMR)

AF:

0.472

AC:

12313

AN:

26088

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

3489

AN:

17238

East Asian (EAS)

AF:

0.652

AC:

20523

AN:

31458

South Asian (SAS)

AF:

0.412

AC:

22464

AN:

54486

European-Finnish (FIN)

AF:

0.357

AC:

14154

AN:

39598

Middle Eastern (MID)

AF:

0.294

AC:

887

AN:

3014

European-Non Finnish (NFE)

AF:

0.211

AC:

114713

AN:

542990

Other (OTH)

AF:

0.273

AC:

9954

AN:

36442

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

6665

13329

19994

26658

33323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2982

5964

8946

11928

14910

<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:

0.308

AC:

46855

AN:

152014

Hom.:

7947

Cov.:

AF XY:

0.324

AC XY:

24050

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.335

AC:

13884

AN:

41452

American (AMR)

AF:

0.405

AC:

6186

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

734

AN:

3468

East Asian (EAS)

AF:

0.602

AC:

3100

AN:

5152

South Asian (SAS)

AF:

0.441

AC:

2123

AN:

4812

European-Finnish (FIN)

AF:

0.391

AC:

4137

AN:

10568

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15659

AN:

67974

Other (OTH)

AF:

0.286

AC:

603

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1612

3223

4835

6446

8058

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.247

Hom.:

7149

Bravo

AF:

0.315

Asia WGS

AF:

0.478

AC:

1661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.1

(source)

DANN

Benign

0.69

PhyloP100

0.58

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