4-140529879-G-A

Variant names:

• chr4-140529879-G-A
• rs2036020
• NM_153702.4:c.171+2385G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153702.4(ELMOD2):​c.171+2385G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,868 control chromosomes in the GnomAD database, including 8,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8286 hom., cov: 32)
• Consequence: ELMOD2 NM_153702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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.171+2385G>A		intron	N/A	NP_714913.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD2	ENST00000323570.8	TSL:1 MANE Select	c.171+2385G>A		intron	N/A	ENSP00000326342.3
	ELMOD2	ENST00000899909.1		c.171+2385G>A		intron	N/A	ENSP00000569968.1
	ELMOD2	ENST00000954139.1		c.171+2385G>A		intron	N/A	ENSP00000624198.1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48996 AN: 151750 Hom.: 8274 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.306

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.323 AC: 49057 AN: 151868 Hom.: 8286 Cov.: 32 AF XY: 0.326 AC XY: 24225 AN XY: 74214

African (AFR) AF: 0.414 AC: 17117 AN: 41362

American (AMR) AF: 0.377 AC: 5746 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2449 AN: 5160

South Asian (SAS) AF: 0.356 AC: 1710 AN: 4810

European-Finnish (FIN) AF: 0.266 AC: 2806 AN: 10532

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

European-Non Finnish (NFE) AF: 0.254 AC: 17261 AN: 67962

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.256 Hom.: 2937

Bravo AF: 0.337

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.32
PhyloP100		-0.54
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: rs2036020; hg19: chr4-141451033;