chr4-140528747-G-A

Variant names:

• chr4-140528747-G-A
• rs3113189
• NM_153702.4:c.171+1253G>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+1253G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,146 control chromosomes in the GnomAD database, including 61,871 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 0.90 (61871 hom., cov: 31)
• Consequence: ELMOD2 NM_153702.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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+1253G>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+1253G>A		intron	N/A	ENSP00000326342.3
	ELMOD2	ENST00000899909.1		c.171+1253G>A		intron	N/A	ENSP00000569968.1
	ELMOD2	ENST00000954139.1		c.171+1253G>A		intron	N/A	ENSP00000624198.1

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136325 AN: 152028 Hom.: 61839 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.946

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.897 AC: 136417 AN: 152146 Hom.: 61871 Cov.: 31 AF XY: 0.896 AC XY: 66660 AN XY: 74376

African (AFR) AF: 0.744 AC: 30821 AN: 41446

American (AMR) AF: 0.946 AC: 14464 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.949 AC: 3296 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5168 AN: 5182

South Asian (SAS) AF: 0.908 AC: 4380 AN: 4824

European-Finnish (FIN) AF: 0.936 AC: 9913 AN: 10596

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65296 AN: 68020

Other (OTH) AF: 0.906 AC: 1912 AN: 2110

Alfa AF: 0.936 Hom.: 13596

Bravo AF: 0.892

Asia WGS AF: 0.927 AC: 3205 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.099
DANN	Benign	0.45
PhyloP100		-2.0
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: rs3113189; hg19: chr4-141449901;