rs11945078

chr4-140524662-G-Achr4-140524662-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153702.4(ELMOD2):c.-10+382G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 984,388 control chromosomes in the GnomAD database, including 36,653 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 (8302 hom., cov: 32)
  • Exomes 𝑓: 0.26 (28351 hom.)
• Consequence: ELMOD2 NM_153702.4 intron
• Scores: Splicing: ADA: 0.0001234
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMOD2	NM_153702.4	c.-10+382G>A		intron_variant		ENST00000323570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMOD2	ENST00000323570.8	c.-10+382G>A		intron_variant		1	NM_153702.4	P1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49058 AN: 152038 Hom.: 8290 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: 0.265

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.305

GnomAD4 exome AF: 0.259 AC: 215221 AN: 832232 Hom.: 28351 Cov.: 29 AF XY: 0.258 AC XY: 99280 AN XY: 384344

Gnomad4 AFR exome AF: 0.427

Gnomad4 AMR exome AF: 0.377

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.461

Gnomad4 SAS exome AF: 0.348

Gnomad4 FIN exome AF: 0.259

Gnomad4 NFE exome AF: 0.251

Gnomad4 OTH exome AF: 0.276

GnomAD4 genome AF: 0.323 AC: 49119 AN: 152156 Hom.: 8302 Cov.: 32 AF XY: 0.326 AC XY: 24278 AN XY: 74396

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.308

Alfa AF: 0.260 Hom.: 5190

Bravo AF: 0.336

Asia WGS AF: 0.407 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	12
Dann	Benign	0.92

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00012
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.070		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: rs11945078; hg19: chr4-141445816;