rs7782979

Variant names:

• chr7-36865445-C-A
• rs7782979
• NM_014800.11:c.1906-3709G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-36865445-C-A
• chr7-36865445-C-G

Variant summary

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

The NM_014800.11(ELMO1):​c.1906-3709G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 152,042 control chromosomes in the GnomAD database, including 16,550 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 0.46 (16550 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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.1906-3709G>T		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1906-3709G>T		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1906-3709G>T		intron	N/A	NP_001193411.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1906-3709G>T		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1906-3709G>T		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000396040.6	TSL:1	c.466-3709G>T		intron	N/A	ENSP00000379355.2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69706 AN: 151924 Hom.: 16545 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.459 AC: 69728 AN: 152042 Hom.: 16550 Cov.: 32 AF XY: 0.459 AC XY: 34112 AN XY: 74330

African (AFR) AF: 0.362 AC: 15005 AN: 41456

American (AMR) AF: 0.408 AC: 6233 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1574 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1739 AN: 5156

South Asian (SAS) AF: 0.402 AC: 1940 AN: 4820

European-Finnish (FIN) AF: 0.596 AC: 6301 AN: 10572

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35464 AN: 67970

Other (OTH) AF: 0.424 AC: 894 AN: 2108

Alfa AF: 0.491 Hom.: 3242

Bravo AF: 0.440

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.44
DANN	Benign	0.51
PhyloP100		-0.57
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: rs7782979; hg19: chr7-36905050;