rs10488029

Positions:

• chr7-37027790-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1301-14355T>C		intron_variant		ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1301-14355T>C		intron_variant		1	NM_014800.11	ENSP00000312185	P1

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

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0625

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0855

Gnomad4 NFE AF: 0.0909

Gnomad4 OTH AF: 0.164

Alfa AF: 0.106 Hom.: 495

Bravo AF: 0.150

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488029; hg19: chr7-37067395;