rs142450830

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_153702.4(ELMOD2):c.428A>C(p.Lys143Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00182 in 1,614,188 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 27 hom. )

Consequence

ELMOD2
NM_153702.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 5.84

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0062583685).

BP6

Variant 4-140540196-A-C is Benign according to our data. Variant chr4-140540196-A-C is described in ClinVar as [Benign]. Clinvar id is 226630.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0032 (488/152340) while in subpopulation EAS AF= 0.0202 (105/5192). AF 95% confidence interval is 0.0171. There are 6 homozygotes in gnomad4. There are 334 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMOD2	NM_153702.4 link	c.428A>C	p.Lys143Thr	missense_variant	Exon 6 of 9	ENST00000323570.8	NP_714913.1	Q8IZ81

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ELMOD2	ENST00000323570.8 link	c.428A>C	p.Lys143Thr	missense_variant	Exon 6 of 9	1	NM_153702.4	ENSP00000326342.3	Q8IZ81
ELMOD2	ENST00000502397.5 link	c.428A>C	p.Lys143Thr	missense_variant	Exon 6 of 6	5		ENSP00000422582.1	D6RBS5
ELMOD2	ENST00000513606.1 link	c.197A>C	p.Lys66Thr	missense_variant	Exon 5 of 5	4		ENSP00000427592.1	D6RHX2
ELMOD2	ENST00000512057.1 link	n.573A>C		non_coding_transcript_exon_variant	Exon 3 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.00321

AC:

489

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0307

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000588

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00435

AC:

1094

AN:

251426

Hom.:

AF XY:

0.00398

AC XY:

541

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.000145

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0210

Gnomad SAS exome

AF:

0.000229

Gnomad FIN exome

AF:

0.0278

Gnomad NFE exome

AF:

0.000633

Gnomad OTH exome

AF:

0.00277

GnomAD4 exome

AF:

0.00168

AC:

2457

AN:

1461848

Hom.:

Cov.:

AF XY:

0.00161

AC XY:

1168

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.000119

Gnomad4 AMR exome

AF:

0.000157

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0187

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.0260

Gnomad4 NFE exome

AF:

0.000156

Gnomad4 OTH exome

AF:

0.00219

GnomAD4 genome

AF:

0.00320

AC:

488

AN:

152340

Hom.:

Cov.:

AF XY:

0.00448

AC XY:

334

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0202

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0307

Gnomad4 NFE

AF:

0.000588

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00122

Hom.:

Bravo

AF:

0.00107

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00404

AC:

490

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Lys143Thr in exon 6 of ELMOD2: This variant is not expected to have clinical sig nificance because it has been identified in 3.6% (7/194) of Han Chinese chromoso mes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.nih .gov/projects/SNP; dbSNP rs142450830). -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.16

T;T;.

Eigen

Benign

-0.20

Eigen_PC

Benign

-0.10

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.80

T;T;T

MetaRNN

Benign

0.0063

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.3

M;.;.

PrimateAI

Benign

0.47

PROVEAN

Uncertain

-2.6

D;D;D

REVEL

Benign

0.099

Sift

Benign

0.042

D;T;T

Sift4G

Benign

0.15

T;T;T

Polyphen

0.0010

B;.;.

Vest4

0.22

MVP

0.16

MPC

0.050

ClinPred

0.035

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.26

gMVP

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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