rs6462733

Variant names:

• chr7-37150779-A-G
• rs6462733
• NM_014800.11:c.1087-17545T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-37150779-A-G
• chr7-37150779-A-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.1087-17545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,102 control chromosomes in the GnomAD database, including 44,060 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 0.74 (44060 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	NM_014800.11	MANE Select	c.1087-17545T>C		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1087-17545T>C		intron	N/A	NP_001193409.1	A4D1X5
	ELMO1	NM_001206482.2		c.1087-17545T>C		intron	N/A	NP_001193411.1	Q92556-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1087-17545T>C		intron	N/A	ENSP00000312185.4	Q92556-1
	ELMO1	ENST00000448602.5	TSL:1	c.1087-17545T>C		intron	N/A	ENSP00000394458.1	Q92556-1
	ELMO1	ENST00000442504.5	TSL:2	c.1087-17545T>C		intron	N/A	ENSP00000406952.1	Q92556-1

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112188 AN: 151984 Hom.: 44061 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.738 AC: 112219 AN: 152102 Hom.: 44060 Cov.: 32 AF XY: 0.741 AC XY: 55115 AN XY: 74362

African (AFR) AF: 0.441 AC: 18284 AN: 41446

American (AMR) AF: 0.803 AC: 12268 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3111 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3676 AN: 5174

South Asian (SAS) AF: 0.836 AC: 4030 AN: 4822

European-Finnish (FIN) AF: 0.854 AC: 9046 AN: 10590

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59205 AN: 68002

Other (OTH) AF: 0.778 AC: 1644 AN: 2112

Alfa AF: 0.837 Hom.: 65836

Bravo AF: 0.722

Asia WGS AF: 0.742 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.36
PhyloP100		0.15
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: rs6462733; hg19: chr7-37190384;