7-36917813-C-T

Variant names:

• chr7-36917813-C-T
• rs2893535
• NM_014800.11:c.1438-22796G>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.1438-22796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,318 control chromosomes in the GnomAD database, including 68,795 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 0.95 (68795 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.1438-22796G>A		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1438-22796G>A		intron	N/A	NP_001193409.1	A4D1X5
	ELMO1	NM_001206482.2		c.1438-22796G>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.1438-22796G>A		intron	N/A	ENSP00000312185.4	Q92556-1
	ELMO1	ENST00000448602.5	TSL:1	c.1438-22796G>A		intron	N/A	ENSP00000394458.1	Q92556-1
	ELMO1	ENST00000396040.6	TSL:1	c.-3-22796G>A		intron	N/A	ENSP00000379355.2	Q92556-2

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144539 AN: 152200 Hom.: 68740 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.950 AC: 144655 AN: 152318 Hom.: 68795 Cov.: 32 AF XY: 0.952 AC XY: 70898 AN XY: 74480

African (AFR) AF: 0.890 AC: 36968 AN: 41554

American (AMR) AF: 0.972 AC: 14871 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5181 AN: 5182

South Asian (SAS) AF: 0.998 AC: 4819 AN: 4828

European-Finnish (FIN) AF: 0.975 AC: 10354 AN: 10624

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65897 AN: 68042

Other (OTH) AF: 0.952 AC: 2015 AN: 2116

Alfa AF: 0.963 Hom.: 112321

Bravo AF: 0.945

Asia WGS AF: 0.989 AC: 3438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.30
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: rs2893535; hg19: chr7-36957418;