7-36918303-T-C

Variant names:

• chr7-36918303-T-C
• rs6942726
• NM_014800.11:c.1438-23286A>G

Variant summary

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

The NM_014800.11(ELMO1):​c.1438-23286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,096 control chromosomes in the GnomAD database, including 5,264 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 0.26 (5264 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 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.1438-23286A>G		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1438-23286A>G		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1438-23286A>G		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.1438-23286A>G		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1438-23286A>G		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000396040.6	TSL:1	c.-3-23286A>G		intron	N/A	ENSP00000379355.2

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39351 AN: 151978 Hom.: 5256 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.259 AC: 39385 AN: 152096 Hom.: 5264 Cov.: 32 AF XY: 0.259 AC XY: 19251 AN XY: 74340

African (AFR) AF: 0.207 AC: 8605 AN: 41496

American (AMR) AF: 0.286 AC: 4366 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1047 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1368 AN: 5180

South Asian (SAS) AF: 0.313 AC: 1511 AN: 4820

European-Finnish (FIN) AF: 0.267 AC: 2825 AN: 10578

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18763 AN: 67960

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.273 Hom.: 7384

Bravo AF: 0.256

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.063
DANN	Benign	0.75
PhyloP100		-0.64
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: rs6942726; hg19: chr7-36957908;