chr7-36912416-A-G

Variant names:

• chr7-36912416-A-G
• rs10488023
• NM_014800.11:c.1438-17399T>C

Variant summary

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

The NM_014800.11(ELMO1):​c.1438-17399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,258 control chromosomes in the GnomAD database, including 1,195 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 0.11 (1195 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 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.1438-17399T>C		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1438-17399T>C		intron	N/A	NP_001193409.1	A4D1X5
	ELMO1	NM_001206482.2		c.1438-17399T>C		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.1438-17399T>C		intron	N/A	ENSP00000312185.4	Q92556-1
	ELMO1	ENST00000448602.5	TSL:1	c.1438-17399T>C		intron	N/A	ENSP00000394458.1	Q92556-1
	ELMO1	ENST00000396040.6	TSL:1	c.-3-17399T>C		intron	N/A	ENSP00000379355.2	Q92556-2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16853 AN: 152140 Hom.: 1197 Cov.: 32

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.111 AC: 16846 AN: 152258 Hom.: 1195 Cov.: 32 AF XY: 0.109 AC XY: 8097 AN XY: 74448

African (AFR) AF: 0.0404 AC: 1679 AN: 41566

American (AMR) AF: 0.163 AC: 2498 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3472

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5184

South Asian (SAS) AF: 0.0711 AC: 343 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1138 AN: 10612

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9999 AN: 67988

Other (OTH) AF: 0.120 AC: 253 AN: 2114

Alfa AF: 0.134 Hom.: 4254

Bravo AF: 0.112

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		0.96
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: rs10488023; hg19: chr7-36952021;