Genetic Variant EME2:c.*63G>T (chr16-1776301-G-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_001257370.2(EME2):c.*63G>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 0.532 in 1,555,992 control chromosomes in the GnomAD database, including 231,827 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 0.44 ( 17362 hom., cov: 33)

Exomes 𝑓: 0.54 ( 214465 hom. )

Consequence

EME2
NM_001257370.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.232

Publications

20 publications found

Variant links:

Genes affected

EME2 (HGNC:27289): (essential meiotic structure-specific endonuclease subunit 2) EME2 forms a heterodimer with MUS81 (MIM 606591) that functions as an XPF (MIM 278760)-type flap/fork endonuclease in DNA repair (Ciccia et al., 2007 [PubMed 17289582]).[supplied by OMIM, Mar 2008]

EME2 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257370.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EME2	NM_001257370.2	MANE Select	c.*63G>T		3_prime_UTR	Exon 8 of 8	NP_001244299.1	A4GXA9-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EME2	ENST00000568449.7	TSL:1 MANE Select	c.*63G>T	3_prime_UTR	Exon 8 of 8	ENSP00000457353.1	A4GXA9-1
EME2	ENST00000561903.6	TSL:2	n.*63G>T	non_coding_transcript_exon	Exon 4 of 6	ENSP00000457966.2	H3BV62
EME2	ENST00000564182.1	TSL:3	n.*63G>T	non_coding_transcript_exon	Exon 2 of 3	ENSP00000456946.1	H3BSZ6

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67341

AN:

151934

Hom.:

17360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.792

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.498

GnomAD4 exome

AF:

0.542

AC:

760559

AN:

1403940

Hom.:

214465

Cov.:

AF XY:

0.534

AC XY:

371001

AN XY:

694612

show subpopulations

African (AFR)

AF:

0.179

AC:

5787

AN:

32254

American (AMR)

AF:

0.645

AC:

26772

AN:

41494

Ashkenazi Jewish (ASJ)

AF:

0.593

AC:

14011

AN:

23610

East Asian (EAS)

AF:

0.281

AC:

10992

AN:

39084

South Asian (SAS)

AF:

0.280

AC:

22771

AN:

81374

European-Finnish (FIN)

AF:

0.487

AC:

24564

AN:

50458

Middle Eastern (MID)

AF:

0.559

AC:

3092

AN:

5528

European-Non Finnish (NFE)

AF:

0.581

AC:

622478

AN:

1072236

Other (OTH)

AF:

0.520

AC:

30092

AN:

57902

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

16491

32982

49474

65965

82456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17086

34172

51258

68344

85430

<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:

0.443

AC:

67351

AN:

152052

Hom.:

17362

Cov.:

AF XY:

0.436

AC XY:

32387

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.185

AC:

7691

AN:

41524

American (AMR)

AF:

0.558

AC:

8537

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

2129

AN:

3472

East Asian (EAS)

AF:

0.323

AC:

1663

AN:

5154

South Asian (SAS)

AF:

0.269

AC:

1298

AN:

4818

European-Finnish (FIN)

AF:

0.471

AC:

4974

AN:

10556

Middle Eastern (MID)

AF:

0.673

AC:

198

AN:

294

European-Non Finnish (NFE)

AF:

0.576

AC:

39099

AN:

67924

Other (OTH)

AF:

0.493

AC:

1041

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1685

3370

5054

6739

8424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.542

Hom.:

23259

Bravo

AF:

0.450

Asia WGS

AF:

0.291

AC:

1011

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.18

(source)

DANN

Benign

0.51

PhyloP100

-0.23

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over