rs3113189

chr4-140528747-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMOD2	NM_153702.4	c.171+1253G>A		intron_variant		ENST00000323570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMOD2	ENST00000323570.8	c.171+1253G>A		intron_variant		1	NM_153702.4	P1
ELMOD2	ENST00000502397.5	c.171+1253G>A		intron_variant		5
ELMOD2	ENST00000513606.1	c.-61+1253G>A		intron_variant		4

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.946

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.906

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.099
Dann	Benign	0.45

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: rs3113189; hg19: chr4-141449901;