Genetic Variant EAF2:p.Gly54Gly (chr3-121844508-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018456.6(EAF2):c.162T>C(p.Gly54Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,608,478 control chromosomes in the GnomAD database, including 26,203 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 0.16 ( 2630 hom., cov: 32)

Exomes 𝑓: 0.16 ( 23573 hom. )

Consequence

EAF2
NM_018456.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

26 publications found

Variant links:

Genes affected

EAF2 (HGNC:23115): (ELL associated factor 2) Enables transcription elongation regulator activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription elongation from RNA polymerase II promoter. Part of transcription elongation factor complex. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Apr 2022]

EAF2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=1.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EAF2	NM_018456.6 link	c.162T>C	p.Gly54Gly	synonymous_variant	Exon 2 of 6	ENST00000273668.7	NP_060926.2	Q96CJ1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EAF2	ENST00000273668.7 link	c.162T>C	p.Gly54Gly	synonymous_variant	Exon 2 of 6	1	NM_018456.6	ENSP00000273668.2		Q96CJ1-1

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24613

AN:

151958

Hom.:

2631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.0813

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.624

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.141

Gnomad OTH

AF:

0.143

GnomAD2 exomes

AF:

0.178

AC:

44261

AN:

248598

AF XY:

0.179

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.128

Gnomad ASJ exome

AF:

0.160

Gnomad EAS exome

AF:

0.641

Gnomad FIN exome

AF:

0.105

Gnomad NFE exome

AF:

0.139

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.158

AC:

230363

AN:

1456402

Hom.:

23573

Cov.:

AF XY:

0.160

AC XY:

115611

AN XY:

724568

show subpopulations

African (AFR)

AF:

0.157

AC:

5216

AN:

33274

American (AMR)

AF:

0.129

AC:

5693

AN:

44130

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

4211

AN:

26016

East Asian (EAS)

AF:

0.646

AC:

25296

AN:

39136

South Asian (SAS)

AF:

0.181

AC:

15521

AN:

85612

European-Finnish (FIN)

AF:

0.107

AC:

5726

AN:

53342

Middle Eastern (MID)

AF:

0.155

AC:

889

AN:

5744

European-Non Finnish (NFE)

AF:

0.142

AC:

157605

AN:

1109008

Other (OTH)

AF:

0.170

AC:

10206

AN:

60140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

7960

15919

23879

31838

39798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5948

11896

17844

23792

29740

<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:

0.162

AC:

24642

AN:

152076

Hom.:

2630

Cov.:

AF XY:

0.164

AC XY:

12161

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.156

AC:

6456

AN:

41492

American (AMR)

AF:

0.151

AC:

2311

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

583

AN:

3466

East Asian (EAS)

AF:

0.624

AC:

3222

AN:

5162

South Asian (SAS)

AF:

0.197

AC:

949

AN:

4820

European-Finnish (FIN)

AF:

0.103

AC:

1086

AN:

10578

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.141

AC:

9608

AN:

67970

Other (OTH)

AF:

0.147

AC:

310

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

993

1986

2978

3971

4964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.150

Hom.:

6412

Bravo

AF:

0.168

Asia WGS

AF:

0.329

AC:

1138

AN:

3472

EpiCase

AF:

0.147

EpiControl

AF:

0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

1.1

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