Variant rs75824346 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_153702.4(ELMOD2):c.*9C>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 0.00145 in 1,585,338 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0014 ( 25 hom. )

Consequence

ELMOD2
NM_153702.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0870

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 4-140550384-C-T is Benign according to our data. Variant chr4-140550384-C-T is described in ClinVar as [Benign]. Clinvar id is 226629.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00137 (1961/1433032) while in subpopulation AMR AF= 0.0259 (999/38644). AF 95% confidence interval is 0.0245. There are 25 homozygotes in gnomad4_exome. There are 880 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ELMOD2	NM_153702.4 link	c.*9C>T	3_prime_UTR_variant	Exon 9 of 9	ENST00000323570.8	NP_714913.1	Q8IZ81
ELMOD2	XM_005262885.4 link	c.*9C>T	3_prime_UTR_variant	Exon 9 of 9		XP_005262942.1
ELMOD2	XM_011531819.3 link	c.*9C>T	3_prime_UTR_variant	Exon 9 of 9		XP_011530121.1	Q8IZ81

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMOD2	ENST00000323570.8 link	c.*9C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_153702.4	ENSP00000326342.3		Q8IZ81
ELMOD2	ENST00000502290.1 link	n.507C>T		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.00226

AC:

344

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0124

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000470

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00566

AC:

1299

AN:

229676

Hom.:

AF XY:

0.00452

AC XY:

563

AN XY:

124474

show subpopulations

Gnomad AFR exome

AF:

0.000922

Gnomad AMR exome

AF:

0.0311

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0150

Gnomad SAS exome

AF:

0.000900

Gnomad FIN exome

AF:

0.00211

Gnomad NFE exome

AF:

0.000584

Gnomad OTH exome

AF:

0.00289

GnomAD4 exome

AF:

0.00137

AC:

1961

AN:

1433032

Hom.:

Cov.:

AF XY:

0.00124

AC XY:

880

AN XY:

711762

show subpopulations

Gnomad4 AFR exome

AF:

0.000438

Gnomad4 AMR exome

AF:

0.0259

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0118

Gnomad4 SAS exome

AF:

0.00102

Gnomad4 FIN exome

AF:

0.00208

Gnomad4 NFE exome

AF:

0.000189

Gnomad4 OTH exome

AF:

0.00142

GnomAD4 genome

AF:

0.00225

AC:

343

AN:

152306

Hom.:

Cov.:

AF XY:

0.00258

AC XY:

192

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.0123

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0135

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.000470

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00118

Hom.:

Bravo

AF:

0.00371

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Oct 12, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

*9C>T in exon 9 of ELMOD2: This variant is not expected to have clinical signifi cance because it has been identified in 3.0% (359/11216), including 5 homozygote s of Latino chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.b roadinstitute.org; dbSNP rs75824346). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.9

DANN

Benign

0.57

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