rs4723619

Variant names:

• chr7-37226747-T-C
• rs4723619
• NM_014800.11:c.550-1717A>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.550-1717A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,208 control chromosomes in the GnomAD database, including 650 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 0.068 (650 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.550-1717A>G		intron_variant	Intron 8 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.550-1717A>G		intron_variant	Intron 8 of 21	1	NM_014800.11	ENSP00000312185.4
ELMO1	ENST00000448602.5	c.550-1717A>G		intron_variant	Intron 8 of 21	1		ENSP00000394458.1
ELMO1	ENST00000442504.5	c.550-1717A>G		intron_variant	Intron 8 of 21	2		ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10280 AN: 152088 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0677 AC: 10309 AN: 152208 Hom.: 650 Cov.: 32 AF XY: 0.0707 AC XY: 5259 AN XY: 74418

African (AFR) AF: 0.0860 AC: 3571 AN: 41532

American (AMR) AF: 0.164 AC: 2499 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1199 AN: 5166

South Asian (SAS) AF: 0.0956 AC: 461 AN: 4822

European-Finnish (FIN) AF: 0.0398 AC: 422 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1920 AN: 68018

Other (OTH) AF: 0.0681 AC: 144 AN: 2114

Alfa AF: 0.0474 Hom.: 1214

Bravo AF: 0.0812

Asia WGS AF: 0.157 AC: 542 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.64
PhyloP100		-1.2
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: rs4723619; hg19: chr7-37266352;