rs3807163

Variant names:

• chr7-36869154-T-C
• rs3807163
• NM_014800.11:c.1905+1239A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-36869154-T-C
• chr7-36869154-T-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.1905+1239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,196 control chromosomes in the GnomAD database, including 6,282 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 0.28 (6282 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1905+1239A>G		intron_variant	Intron 20 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1905+1239A>G		intron_variant	Intron 20 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43254 AN: 152078 Hom.: 6265 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.284 AC: 43292 AN: 152196 Hom.: 6282 Cov.: 32 AF XY: 0.284 AC XY: 21145 AN XY: 74406

African (AFR) AF: 0.267 AC: 11091 AN: 41524

American (AMR) AF: 0.310 AC: 4736 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1199 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5178

South Asian (SAS) AF: 0.316 AC: 1525 AN: 4822

European-Finnish (FIN) AF: 0.302 AC: 3192 AN: 10580

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19337 AN: 68014

Other (OTH) AF: 0.296 AC: 626 AN: 2112

Alfa AF: 0.222 Hom.: 838

Bravo AF: 0.283

Asia WGS AF: 0.308 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.21
PhyloP100		-1.6
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: rs3807163; hg19: chr7-36908759;