rs2041801

Variant names:

• chr7-36887236-G-A
• rs2041801
• NM_014800.11:c.1714+324C>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.1714+324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,034 control chromosomes in the GnomAD database, including 17,311 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 (17311 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• 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

LOC105375235 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1714+324C>T		intron_variant	Intron 18 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1714+324C>T		intron_variant	Intron 18 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69252 AN: 151916 Hom.: 17309 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.456 AC: 69261 AN: 152034 Hom.: 17311 Cov.: 32 AF XY: 0.456 AC XY: 33873 AN XY: 74308

African (AFR) AF: 0.258 AC: 10714 AN: 41478

American (AMR) AF: 0.434 AC: 6629 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1795 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1711 AN: 5170

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4814

European-Finnish (FIN) AF: 0.619 AC: 6536 AN: 10566

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38337 AN: 67948

Other (OTH) AF: 0.445 AC: 938 AN: 2110

Alfa AF: 0.515 Hom.: 58893

Bravo AF: 0.432

Asia WGS AF: 0.350 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.59
DANN	Benign	0.50
PhyloP100		-1.1
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: rs2041801; hg19: chr7-36926841; COSMIC: COSV60302557;