chr7-36878390-C-T

Variant names:

• chr7-36878390-C-T
• rs741301
• NM_014800.11:c.1715-273G>A

Variant summary

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

The NM_014800.11(ELMO1):​c.1715-273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,862 control chromosomes in the GnomAD database, including 27,490 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 0.59 (27490 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 41 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 (NFE) allele frequency at 95% confidence interval = 0.668 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.1715-273G>A		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1715-273G>A		intron	N/A	NP_001193409.1	A4D1X5
	ELMO1	NM_001206482.2		c.1715-273G>A		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.1715-273G>A		intron	N/A	ENSP00000312185.4	Q92556-1
	ELMO1	ENST00000448602.5	TSL:1	c.1715-273G>A		intron	N/A	ENSP00000394458.1	Q92556-1
	ELMO1	ENST00000396040.6	TSL:1	c.275-273G>A		intron	N/A	ENSP00000379355.2	Q92556-2

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89690 AN: 151742 Hom.: 27471 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.591 AC: 89736 AN: 151862 Hom.: 27490 Cov.: 31 AF XY: 0.592 AC XY: 43917 AN XY: 74228

African (AFR) AF: 0.423 AC: 17498 AN: 41380

American (AMR) AF: 0.565 AC: 8626 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2199 AN: 3472

East Asian (EAS) AF: 0.670 AC: 3450 AN: 5152

South Asian (SAS) AF: 0.628 AC: 3015 AN: 4804

European-Finnish (FIN) AF: 0.684 AC: 7197 AN: 10524

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45774 AN: 67956

Other (OTH) AF: 0.597 AC: 1263 AN: 2114

Alfa AF: 0.637 Hom.: 83756

Bravo AF: 0.576

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.42
PhyloP100		-0.53
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: rs741301; hg19: chr7-36917995;