7-37161008-G-A

Variant names:

• chr7-37161008-G-A
• rs1345365
• NM_014800.11:c.1087-27774C>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.1087-27774C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,990 control chromosomes in the GnomAD database, including 31,297 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 0.62 (31297 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 19 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1087-27774C>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.1087-27774C>T		intron_variant	Intron 13 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93996 AN: 151872 Hom.: 31303 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.619 AC: 94009 AN: 151990 Hom.: 31297 Cov.: 31 AF XY: 0.623 AC XY: 46254 AN XY: 74296

African (AFR) AF: 0.347 AC: 14362 AN: 41410

American (AMR) AF: 0.661 AC: 10095 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2556 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3612 AN: 5164

South Asian (SAS) AF: 0.605 AC: 2908 AN: 4806

European-Finnish (FIN) AF: 0.790 AC: 8351 AN: 10576

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.735 AC: 49958 AN: 67972

Other (OTH) AF: 0.636 AC: 1344 AN: 2112

Alfa AF: 0.702 Hom.: 64007

Bravo AF: 0.602

Asia WGS AF: 0.629 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.023
DANN	Benign	0.86
PhyloP100		-1.2
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: rs1345365; hg19: chr7-37200613;