rs11769038

Variant names:

• chr7-36903709-G-T
• rs11769038
• NM_014800.11:c.1438-8692C>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.1438-8692C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,036 control chromosomes in the GnomAD database, including 16,948 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 0.45 (16948 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 8 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1438-8692C>A		intron_variant	Intron 16 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1438-8692C>A		intron_variant	Intron 16 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68648 AN: 151918 Hom.: 16947 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.452 AC: 68658 AN: 152036 Hom.: 16948 Cov.: 32 AF XY: 0.450 AC XY: 33473 AN XY: 74306

African (AFR) AF: 0.266 AC: 11031 AN: 41472

American (AMR) AF: 0.426 AC: 6505 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1507 AN: 5166

South Asian (SAS) AF: 0.398 AC: 1916 AN: 4816

European-Finnish (FIN) AF: 0.591 AC: 6240 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38097 AN: 67954

Other (OTH) AF: 0.445 AC: 940 AN: 2110

Alfa AF: 0.489 Hom.: 6518

Bravo AF: 0.430

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.86
PhyloP100		1.0
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: rs11769038; hg19: chr7-36943314;