chr7-36861974-T-C

Variant names:

• chr7-36861974-T-C
• rs7785934
• NM_014800.11:c.1906-238A>G

Variant summary

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

The NM_014800.11(ELMO1):​c.1906-238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 535,124 control chromosomes in the GnomAD database, including 51,111 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 0.41 (13480 hom., cov: 31)
  • Exomes 𝑓: 0.44 (37631 hom.)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 10 publications found

Genes affected

ELMO1 (HGNC:16286): (engulfment and cell motility 1) This gene encodes a member of the engulfment and cell motility protein family. These proteins interact with dedicator of cytokinesis proteins to promote phagocytosis and cell migration. Increased expression of this gene and dedicator of cytokinesis 1 may promote glioma cell invasion, and single nucleotide polymorphisms in this gene may be associated with diabetic nephropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ELMO1 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014800.11. 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
	ELMO1	NM_014800.11	MANE Select	c.1906-238A>G		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1906-238A>G		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1906-238A>G		intron	N/A	NP_001193411.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1906-238A>G		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1906-238A>G		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000396040.6	TSL:1	c.466-238A>G		intron	N/A	ENSP00000379355.2

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62871 AN: 151832 Hom.: 13474 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.438 AC: 167777 AN: 383174 Hom.: 37631 Cov.: 3 AF XY: 0.434 AC XY: 87514 AN XY: 201538

African (AFR) AF: 0.331 AC: 3801 AN: 11468

American (AMR) AF: 0.344 AC: 6093 AN: 17726

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 4683 AN: 11882

East Asian (EAS) AF: 0.331 AC: 9292 AN: 28082

South Asian (SAS) AF: 0.370 AC: 13801 AN: 37286

European-Finnish (FIN) AF: 0.482 AC: 12177 AN: 25286

Middle Eastern (MID) AF: 0.371 AC: 650 AN: 1752

European-Non Finnish (NFE) AF: 0.474 AC: 107799 AN: 227332

Other (OTH) AF: 0.424 AC: 9481 AN: 22360

GnomAD4 genome AF: 0.414 AC: 62885 AN: 151950 Hom.: 13480 Cov.: 31 AF XY: 0.412 AC XY: 30566 AN XY: 74248

African (AFR) AF: 0.326 AC: 13534 AN: 41466

American (AMR) AF: 0.349 AC: 5319 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1820 AN: 5164

South Asian (SAS) AF: 0.385 AC: 1848 AN: 4804

European-Finnish (FIN) AF: 0.492 AC: 5183 AN: 10542

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32470 AN: 67934

Other (OTH) AF: 0.389 AC: 820 AN: 2110

Alfa AF: 0.448 Hom.: 19887

Bravo AF: 0.400

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		0.12
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: rs7785934; hg19: chr7-36901579;