NM_014800.11:c.1086+34667C>T

Variant names:

• chr7-37176719-G-A
• rs7782590
• NM_014800.11:c.1086+34667C>T

Variant summary

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

The NM_014800.11(ELMO1):​c.1086+34667C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,206 control chromosomes in the GnomAD database, including 58,524 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 0.87 (58524 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	NM_014800.11	MANE Select	c.1086+34667C>T		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1086+34667C>T		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1086+34667C>T		intron	N/A	NP_001193411.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1086+34667C>T		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1086+34667C>T		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.1086+34667C>T		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131940 AN: 152088 Hom.: 58507 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.867 AC: 131996 AN: 152206 Hom.: 58524 Cov.: 33 AF XY: 0.870 AC XY: 64709 AN XY: 74418

African (AFR) AF: 0.662 AC: 27467 AN: 41472

American (AMR) AF: 0.888 AC: 13571 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3398 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4242 AN: 5166

South Asian (SAS) AF: 0.931 AC: 4497 AN: 4830

European-Finnish (FIN) AF: 0.972 AC: 10323 AN: 10624

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65475 AN: 68034

Other (OTH) AF: 0.893 AC: 1889 AN: 2116

Alfa AF: 0.912 Hom.: 7982

Bravo AF: 0.850

Asia WGS AF: 0.851 AC: 2960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.48
PhyloP100		0.43
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: rs7782590; hg19: chr7-37216324;