rs10488029

Variant names:

• chr7-37027790-A-G
• rs10488029
• NM_014800.11:c.1301-14355T>C

Variant summary

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

The NM_014800.11(ELMO1):​c.1301-14355T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,876 control chromosomes in the GnomAD database, including 1,728 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 0.14 (1728 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	NM_014800.11	MANE Select	c.1301-14355T>C		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1301-14355T>C		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1301-14355T>C		intron	N/A	NP_001193411.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.1301-14355T>C		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1301-14355T>C		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.1301-14355T>C		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20809 AN: 151760 Hom.: 1729 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0908

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.137 AC: 20819 AN: 151876 Hom.: 1728 Cov.: 31 AF XY: 0.138 AC XY: 10253 AN XY: 74242

African (AFR) AF: 0.227 AC: 9390 AN: 41384

American (AMR) AF: 0.156 AC: 2376 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.0625 AC: 321 AN: 5132

South Asian (SAS) AF: 0.143 AC: 687 AN: 4806

European-Finnish (FIN) AF: 0.0855 AC: 903 AN: 10560

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6174 AN: 67952

Other (OTH) AF: 0.164 AC: 346 AN: 2106

Alfa AF: 0.128 Hom.: 1257

Bravo AF: 0.150

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.39
PhyloP100		-0.25
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: rs10488029; hg19: chr7-37067395;