chr7-37347046-G-C

Variant names:

• chr7-37347046-G-C
• rs1986567
• NM_014800.11:c.-73-4283C>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.-73-4283C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,944 control chromosomes in the GnomAD database, including 24,567 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 0.57 (24567 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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.-73-4283C>G		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.-73-4283C>G		intron	N/A	NP_001193409.1	A4D1X5
	ELMO1	NM_001206482.2		c.-73-4283C>G		intron	N/A	NP_001193411.1	Q92556-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.-73-4283C>G		intron	N/A	ENSP00000312185.4	Q92556-1
	ELMO1	ENST00000448602.5	TSL:1	c.-73-4283C>G		intron	N/A	ENSP00000394458.1	Q92556-1
	ELMO1	ENST00000442504.5	TSL:2	c.-73-4283C>G		intron	N/A	ENSP00000406952.1	Q92556-1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86116 AN: 151826 Hom.: 24543 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.567 AC: 86197 AN: 151944 Hom.: 24567 Cov.: 31 AF XY: 0.569 AC XY: 42241 AN XY: 74260

African (AFR) AF: 0.609 AC: 25235 AN: 41444

American (AMR) AF: 0.525 AC: 8014 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1610 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3444 AN: 5164

South Asian (SAS) AF: 0.631 AC: 3033 AN: 4806

European-Finnish (FIN) AF: 0.543 AC: 5735 AN: 10560

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37350 AN: 67924

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.568 Hom.: 3045

Bravo AF: 0.566

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.47
PhyloP100		0.57
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: rs1986567; hg19: chr7-37386650;