dbSNP rs882930: ELMOD2:c.270-81T>G (chr4-140537331-T-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.270-81T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 1,224,476 control chromosomes in the GnomAD database, including 270,707 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 25445 hom., cov: 31)

Exomes 𝑓: 0.67 ( 245262 hom. )

Consequence

ELMOD2
NM_153702.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.217

Publications

4 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:

Genome browser will be placed here

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=-0.75).

BP6

Variant 4-140537331-T-G is Benign according to our data. Variant chr4-140537331-T-G is described in ClinVar as Benign. ClinVar VariationId is 1235399.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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.270-81T>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.270-81T>G	intron	N/A	ENSP00000326342.3	Q8IZ81
ELMOD2	ENST00000899909.1		c.315-81T>G	intron	N/A	ENSP00000569968.1
ELMOD2	ENST00000954139.1		c.315-81T>G	intron	N/A	ENSP00000624198.1

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

84416

AN:

151852

Hom.:

25440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.560

Gnomad ASJ

AF:

0.631

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.514

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.574

GnomAD4 exome

AF:

0.671

AC:

719894

AN:

1072506

Hom.:

245262

AF XY:

0.669

AC XY:

352333

AN XY:

526828

show subpopulations

African (AFR)

AF:

0.295

AC:

6260

AN:

21256

American (AMR)

AF:

0.562

AC:

6076

AN:

10804

Ashkenazi Jewish (ASJ)

AF:

0.643

AC:

10812

AN:

16818

East Asian (EAS)

AF:

0.539

AC:

14858

AN:

27562

South Asian (SAS)

AF:

0.528

AC:

24445

AN:

46312

European-Finnish (FIN)

AF:

0.670

AC:

20994

AN:

31356

Middle Eastern (MID)

AF:

0.612

AC:

2499

AN:

4082

European-Non Finnish (NFE)

AF:

0.696

AC:

604930

AN:

869032

Other (OTH)

AF:

0.641

AC:

29020

AN:

45284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

10610

21221

31831

42442

53052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15496

30992

46488

61984

77480

<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:

0.556

AC:

84453

AN:

151970

Hom.:

25445

Cov.:

AF XY:

0.552

AC XY:

40994

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.309

AC:

12806

AN:

41438

American (AMR)

AF:

0.560

AC:

8552

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

2188

AN:

3468

East Asian (EAS)

AF:

0.492

AC:

2545

AN:

5174

South Asian (SAS)

AF:

0.514

AC:

2475

AN:

4814

European-Finnish (FIN)

AF:

0.661

AC:

6967

AN:

10548

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.690

AC:

46917

AN:

67956

Other (OTH)

AF:

0.574

AC:

1208

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1729

3458

5186

6915

8644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

716

1432

2148

2864

3580

<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:

0.592

Hom.:

4329

Bravo

AF:

0.538

Asia WGS

AF:

0.481

AC:

1669

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

-0.75

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

-0.22

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