NM_014800.11:c.1087-17036G>A

Variant names:

• chr7-37150270-C-T
• rs6967682
• NM_014800.11:c.1087-17036G>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.1087-17036G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 147,226 control chromosomes in the GnomAD database, including 43,852 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 0.76 (43852 hom., cov: 29)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1087-17036G>A		intron_variant	Intron 13 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1087-17036G>A		intron_variant	Intron 13 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 111661 AN: 147120 Hom.: 43853 Cov.: 29

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.759 AC: 111691 AN: 147226 Hom.: 43852 Cov.: 29 AF XY: 0.762 AC XY: 54769 AN XY: 71848

African (AFR) AF: 0.481 AC: 18141 AN: 37744

American (AMR) AF: 0.810 AC: 12231 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3105 AN: 3446

East Asian (EAS) AF: 0.717 AC: 3663 AN: 5108

South Asian (SAS) AF: 0.840 AC: 3994 AN: 4752

European-Finnish (FIN) AF: 0.865 AC: 8823 AN: 10200

Middle Eastern (MID) AF: 0.752 AC: 206 AN: 274

European-Non Finnish (NFE) AF: 0.874 AC: 59156 AN: 67648

Other (OTH) AF: 0.795 AC: 1629 AN: 2050

Alfa AF: 0.846 Hom.: 23578

Bravo AF: 0.721

Asia WGS AF: 0.741 AC: 2570 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.7
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: rs6967682; hg19: chr7-37189875;