rs11945078

Variant names:

• chr4-140524662-G-A
• rs11945078
• NM_153702.4:c.-10+382G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-140524662-G-A
• chr4-140524662-G-C

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD2	NM_153702.4	MANE Select	c.-10+382G>A		intron	N/A	NP_714913.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD2	ENST00000323570.8	TSL:1 MANE Select	c.-10+382G>A		intron	N/A	ENSP00000326342.3
	ELMOD2	ENST00000503541.1	TSL:2	n.445G>A		non_coding_transcript_exon	Exon 1 of 2
	ELMOD2	ENST00000502397.5	TSL:5	c.-10+1G>A		splice_donor intron	N/A	ENSP00000422582.1

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

African (AFR) AF: 0.427 AC: 6725 AN: 15764

American (AMR) AF: 0.377 AC: 369 AN: 980

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 1401 AN: 5148

East Asian (EAS) AF: 0.461 AC: 1672 AN: 3628

South Asian (SAS) AF: 0.348 AC: 5724 AN: 16446

European-Finnish (FIN) AF: 0.259 AC: 74 AN: 286

Middle Eastern (MID) AF: 0.241 AC: 390 AN: 1620

European-Non Finnish (NFE) AF: 0.251 AC: 191346 AN: 761084

Other (OTH) AF: 0.276 AC: 7520 AN: 27276

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

African (AFR) AF: 0.414 AC: 17162 AN: 41500

American (AMR) AF: 0.376 AC: 5756 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2460 AN: 5172

South Asian (SAS) AF: 0.355 AC: 1712 AN: 4826

European-Finnish (FIN) AF: 0.265 AC: 2808 AN: 10588

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17256 AN: 67986

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.272 Hom.: 7467

Bravo AF: 0.336

Asia WGS AF: 0.407 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.92
PhyloP100		-0.14
PromoterAI		0.022	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11945078; hg19: chr4-141445816;