rs10488031

Variant names:

• chr7-37037249-G-A
• rs10488031
• NM_014800.11:c.1301-23814C>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.1301-23814C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,234 control chromosomes in the GnomAD database, including 814 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 0.092 (814 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1301-23814C>T		intron_variant	Intron 15 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1301-23814C>T		intron_variant	Intron 15 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13953 AN: 152116 Hom.: 810 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0918 AC: 13981 AN: 152234 Hom.: 814 Cov.: 32 AF XY: 0.0899 AC XY: 6688 AN XY: 74424

African (AFR) AF: 0.168 AC: 6963 AN: 41528

American (AMR) AF: 0.0600 AC: 917 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3468

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5178

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4820

European-Finnish (FIN) AF: 0.0599 AC: 635 AN: 10602

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0682 AC: 4642 AN: 68024

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0754 Hom.: 1887

Bravo AF: 0.0950

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.59
PhyloP100		-0.11
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: rs10488031; hg19: chr7-37076854;