Variant 4-140525613-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153702.4(ELMOD2):c.142+43G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 1,564,094 control chromosomes in the GnomAD database, including 62,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8292 hom., cov: 32)

Exomes 𝑓: 0.27 ( 54231 hom. )

Consequence

ELMOD2
NM_153702.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.374

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:

ELMOD2 (HGNC:):

ELMOD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 4-140525613-G-T is Benign according to our data. Variant chr4-140525613-G-T is described in ClinVar as [Benign]. Clinvar id is 1264141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMOD2	NM_153702.4 linkuse as main transcript	c.142+43G>T		intron_variant		ENST00000323570.8	NP_714913.1	Q8IZ81

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ELMOD2	ENST00000323570.8 linkuse as main transcript	c.142+43G>T	intron_variant	1	NM_153702.4	ENSP00000326342.3	Q8IZ81
ELMOD2	ENST00000502397.5 linkuse as main transcript	c.142+43G>T	intron_variant	5		ENSP00000422582.1	D6RBS5
ELMOD2	ENST00000511887.6 linkuse as main transcript	c.142+43G>T	intron_variant	4		ENSP00000476419.1	V9GY58
ELMOD2	ENST00000503541.1 linkuse as main transcript	n.1353+43G>T	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49021

AN:

151866

Hom.:

8280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.306

GnomAD3 exomes

AF:

0.314

AC:

65867

AN:

209956

Hom.:

10760

AF XY:

0.309

AC XY:

35443

AN XY:

114598

show subpopulations

Gnomad AFR exome

AF:

0.419

Gnomad AMR exome

AF:

0.405

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.470

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.292

GnomAD4 exome

AF:

0.272

AC:

383650

AN:

1412110

Hom.:

54231

Cov.:

AF XY:

0.273

AC XY:

191256

AN XY:

701082

show subpopulations

Gnomad4 AFR exome

AF:

0.422

Gnomad4 AMR exome

AF:

0.394

Gnomad4 ASJ exome

AF:

0.268

Gnomad4 EAS exome

AF:

0.439

Gnomad4 SAS exome

AF:

0.340

Gnomad4 FIN exome

AF:

0.267

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.323

AC:

49082

AN:

151984

Hom.:

8292

Cov.:

AF XY:

0.326

AC XY:

24258

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.414

Gnomad4 AMR

AF:

0.376

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.354

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.286

Hom.:

1476

Bravo

AF:

0.337

Asia WGS

AF:

0.405

AC:

1409

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

DANN

Benign

0.64

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over