7-37172699-C-A

Variant names:

• chr7-37172699-C-A
• rs1981740
• NM_014800.11:c.1086+38687G>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.1086+38687G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,146 control chromosomes in the GnomAD database, including 40,434 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 0.70 (40434 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1086+38687G>T		intron_variant	Intron 13 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1086+38687G>T		intron_variant	Intron 13 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107027 AN: 152028 Hom.: 40438 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.704 AC: 107045 AN: 152146 Hom.: 40434 Cov.: 33 AF XY: 0.708 AC XY: 52677 AN XY: 74380

African (AFR) AF: 0.398 AC: 16493 AN: 41440

American (AMR) AF: 0.776 AC: 11866 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3015 AN: 3472

East Asian (EAS) AF: 0.738 AC: 3829 AN: 5186

South Asian (SAS) AF: 0.813 AC: 3918 AN: 4822

European-Finnish (FIN) AF: 0.833 AC: 8817 AN: 10588

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56634 AN: 68022

Other (OTH) AF: 0.741 AC: 1569 AN: 2116

Alfa AF: 0.743 Hom.: 5691

Bravo AF: 0.687

Asia WGS AF: 0.741 AC: 2579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.68
PhyloP100		-0.16
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: rs1981740; hg19: chr7-37212304;