NM_153702.4:c.142+43G>T

Variant names:

• chr4-140525613-G-T
• rs3828535
• NM_153702.4:c.142+43G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong 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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.374
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

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.142+43G>T		intron	N/A	NP_714913.1	Q8IZ81

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD2	ENST00000323570.8	TSL:1 MANE Select	c.142+43G>T		intron	N/A	ENSP00000326342.3	Q8IZ81
	ELMOD2	ENST00000899909.1		c.142+43G>T		intron	N/A	ENSP00000569968.1
	ELMOD2	ENST00000954139.1		c.142+43G>T		intron	N/A	ENSP00000624198.1

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

GnomAD2 exomes AF: 0.314 AC: 65867 AN: 209956 AF XY: 0.309

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 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

African (AFR) AF: 0.422 AC: 12898 AN: 30598

American (AMR) AF: 0.394 AC: 13485 AN: 34260

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 6406 AN: 23896

East Asian (EAS) AF: 0.439 AC: 16791 AN: 38236

South Asian (SAS) AF: 0.340 AC: 26652 AN: 78320

European-Finnish (FIN) AF: 0.267 AC: 13840 AN: 51830

Middle Eastern (MID) AF: 0.239 AC: 1329 AN: 5556

European-Non Finnish (NFE) AF: 0.253 AC: 275671 AN: 1091276

Other (OTH) AF: 0.285 AC: 16578 AN: 58138

GnomAD4 genome AF: 0.323 AC: 49082 AN: 151984 Hom.: 8292 Cov.: 32 AF XY: 0.326 AC XY: 24258 AN XY: 74308

African (AFR) AF: 0.414 AC: 17128 AN: 41406

American (AMR) AF: 0.376 AC: 5751 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3464

East Asian (EAS) AF: 0.475 AC: 2457 AN: 5172

South Asian (SAS) AF: 0.354 AC: 1709 AN: 4824

European-Finnish (FIN) AF: 0.266 AC: 2810 AN: 10576

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17265 AN: 67952

Other (OTH) AF: 0.308 AC: 648 AN: 2102

Alfa AF: 0.289 Hom.: 1546

Bravo AF: 0.337

Asia WGS AF: 0.405 AC: 1409 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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