NM_014800.11:c.79-9632C>T

Variant names:

• chr7-37325592-G-A
• rs2392492
• NM_014800.11:c.79-9632C>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.79-9632C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0374 in 152,098 control chromosomes in the GnomAD database, including 148 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 0.037 (148 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0582 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.79-9632C>T		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.79-9632C>T		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.79-9632C>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.79-9632C>T		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.79-9632C>T		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.79-9632C>T		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.0374 AC: 5690 AN: 151980 Hom.: 148 Cov.: 32

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0460

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0374 AC: 5687 AN: 152098 Hom.: 148 Cov.: 32 AF XY: 0.0349 AC XY: 2595 AN XY: 74346

African (AFR) AF: 0.0107 AC: 445 AN: 41490

American (AMR) AF: 0.0459 AC: 702 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4820

European-Finnish (FIN) AF: 0.0141 AC: 149 AN: 10564

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4059 AN: 67992

Other (OTH) AF: 0.0422 AC: 89 AN: 2108

Alfa AF: 0.0456 Hom.: 198

Bravo AF: 0.0389

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.76
DANN	Benign	0.72
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism

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: rs2392492; hg19: chr7-37365196;