rs2541095

Variant names:

• chr7-37131296-T-C
• rs2541095
• NM_014800.11:c.1191+1834A>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.1191+1834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,064 control chromosomes in the GnomAD database, including 2,650 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 0.17 (2650 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1191+1834A>G		intron_variant	Intron 14 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1191+1834A>G		intron_variant	Intron 14 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26489 AN: 151946 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.174 AC: 26519 AN: 152064 Hom.: 2650 Cov.: 32 AF XY: 0.170 AC XY: 12625 AN XY: 74308

African (AFR) AF: 0.277 AC: 11481 AN: 41452

American (AMR) AF: 0.185 AC: 2819 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5174

South Asian (SAS) AF: 0.120 AC: 577 AN: 4818

European-Finnish (FIN) AF: 0.0788 AC: 835 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8629 AN: 67972

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.137 Hom.: 849

Bravo AF: 0.187

Asia WGS AF: 0.175 AC: 607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.62
PhyloP100		-0.35
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: rs2541095; hg19: chr7-37170901;