7-37195151-T-C

Variant names:

• chr7-37195151-T-C
• rs2058730
• NM_014800.11:c.1086+16235A>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.1086+16235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,976 control chromosomes in the GnomAD database, including 23,179 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 0.53 (23179 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1086+16235A>G		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.1086+16235A>G		intron_variant	Intron 13 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81111 AN: 151860 Hom.: 23175 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.534 AC: 81131 AN: 151976 Hom.: 23179 Cov.: 31 AF XY: 0.531 AC XY: 39478 AN XY: 74290

African (AFR) AF: 0.319 AC: 13240 AN: 41462

American (AMR) AF: 0.530 AC: 8087 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3466

East Asian (EAS) AF: 0.651 AC: 3350 AN: 5148

South Asian (SAS) AF: 0.500 AC: 2407 AN: 4816

European-Finnish (FIN) AF: 0.607 AC: 6408 AN: 10552

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43804 AN: 67942

Other (OTH) AF: 0.546 AC: 1155 AN: 2116

Alfa AF: 0.596 Hom.: 34554

Bravo AF: 0.521

Asia WGS AF: 0.552 AC: 1921 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.70
PhyloP100		-0.36
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: rs2058730; hg19: chr7-37234756;