7-37147952-T-G

Variant names:

• chr7-37147952-T-G
• rs6462731
• NM_014800.11:c.1087-14718A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014800.11(ELMO1):​c.1087-14718A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,114 control chromosomes in the GnomAD database, including 53,948 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 0.84 (53948 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.9 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.1087-14718A>C		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1087-14718A>C		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1087-14718A>C		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.1087-14718A>C		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1087-14718A>C		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.1087-14718A>C		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127116 AN: 151996 Hom.: 53930 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.836 AC: 127183 AN: 152114 Hom.: 53948 Cov.: 31 AF XY: 0.840 AC XY: 62449 AN XY: 74360

African (AFR) AF: 0.688 AC: 28490 AN: 41412

American (AMR) AF: 0.839 AC: 12820 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3472

East Asian (EAS) AF: 0.777 AC: 4020 AN: 5174

South Asian (SAS) AF: 0.900 AC: 4347 AN: 4830

European-Finnish (FIN) AF: 0.938 AC: 9948 AN: 10608

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61600 AN: 68012

Other (OTH) AF: 0.839 AC: 1772 AN: 2112

Alfa AF: 0.881 Hom.: 17726

Bravo AF: 0.821

Asia WGS AF: 0.821 AC: 2857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		-0.073
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: rs6462731; hg19: chr7-37187557;