Genetic Variant ELMOD2:c.-9-294A>G (chr4-140525126-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153702.4(ELMOD2):c.-9-294A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 216,048 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 575 hom., cov: 33)

Exomes 𝑓: 0.071 ( 169 hom. )

Consequence

ELMOD2
NM_153702.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.73

Publications

0 publications found

Variant links:

Genes affected

ELMOD2 (HGNC:28111): (ELMO domain containing 2) This gene encodes one of six engulfment and motility (ELMO) domain-containing proteins. This gene is thought to play a role in antiviral responses. Mutations in this gene may be involved in the cause of familial idiopathic pulmonary fibrosis. [provided by RefSeq, Sep 2010]

ELMOD2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 4-140525126-A-G is Benign according to our data. Variant chr4-140525126-A-G is described in ClinVar as Benign. ClinVar VariationId is 1280946.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153702.4. 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
	ELMOD2	NM_153702.4	MANE Select	c.-9-294A>G		intron	N/A	NP_714913.1	Q8IZ81

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ELMOD2	ENST00000323570.8	TSL:1 MANE Select	c.-9-294A>G	intron	N/A	ENSP00000326342.3	Q8IZ81
ELMOD2	ENST00000899909.1		c.-9-294A>G	intron	N/A	ENSP00000569968.1
ELMOD2	ENST00000954139.1		c.-9-294A>G	intron	N/A	ENSP00000624198.1

Frequencies

GnomAD3 genomes

AF:

0.0858

AC:

13062

AN:

152190

Hom.:

576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0963

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0982

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.0702

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.0852

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0757

Gnomad OTH

AF:

0.0870

GnomAD4 exome

AF:

0.0712

AC:

4536

AN:

63740

Hom.:

169

Cov.:

AF XY:

0.0716

AC XY:

2412

AN XY:

33704

show subpopulations

African (AFR)

AF:

0.0900

AC:

149

AN:

1656

American (AMR)

AF:

0.0925

AC:

210

AN:

2270

Ashkenazi Jewish (ASJ)

AF:

0.0888

AC:

188

AN:

2118

East Asian (EAS)

AF:

0.0615

AC:

193

AN:

3140

South Asian (SAS)

AF:

0.0873

AC:

564

AN:

6458

European-Finnish (FIN)

AF:

0.0757

AC:

185

AN:

2444

Middle Eastern (MID)

AF:

0.0767

AC:

AN:

300

European-Non Finnish (NFE)

AF:

0.0667

AC:

2768

AN:

41526

Other (OTH)

AF:

0.0669

AC:

256

AN:

3828

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

210

421

631

842

1052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0858

AC:

13074

AN:

152308

Hom.:

575

Cov.:

AF XY:

0.0874

AC XY:

6508

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.0966

AC:

4013

AN:

41556

American (AMR)

AF:

0.0978

AC:

1496

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

351

AN:

3470

East Asian (EAS)

AF:

0.0699

AC:

363

AN:

5190

South Asian (SAS)

AF:

0.108

AC:

523

AN:

4830

European-Finnish (FIN)

AF:

0.0852

AC:

904

AN:

10612

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0757

AC:

5150

AN:

68026

Other (OTH)

AF:

0.0866

AC:

183

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

612

1224

1837

2449

3061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0851

Hom.:

Bravo

AF:

0.0869

Asia WGS

AF:

0.0820

AC:

287

AN:

3474

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.2

(source)

DANN

Benign

0.78

PhyloP100

1.7

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