4-140525613-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.374

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	UniProt
ELMOD2	NM_153702.4	c.142+43G>T		intron_variant		ENST00000323570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMOD2	ENST00000323570.8	c.142+43G>T		intron_variant		1	NM_153702.4	P1
ELMOD2	ENST00000502397.5	c.142+43G>T		intron_variant		5
ELMOD2	ENST00000511887.6	c.142+43G>T		intron_variant		4
ELMOD2	ENST00000503541.1	n.1353+43G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49021 AN: 151866 Hom.: 8280 Cov.: 32

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

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.: 28 AF XY: 0.273 AC XY: 191256 AN XY: 701082

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.: 32 AF XY: 0.326 AC XY: 24258 AN XY: 74308

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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

Other links and lift over

dbSNP: rs3828535; hg19: chr4-141446767; COSMIC: COSV60271325; COSMIC: COSV60271325;