rs10488023

Positions:

• chr7-36912416-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.1438-17399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,258 control chromosomes in the GnomAD database, including 1,195 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 0.11 (1195 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1438-17399T>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.1438-17399T>C		intron_variant		1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16853 AN: 152140 Hom.: 1197 Cov.: 32

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0717

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.111 AC: 16846 AN: 152258 Hom.: 1195 Cov.: 32 AF XY: 0.109 AC XY: 8097 AN XY: 74448

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.120

Alfa AF: 0.140 Hom.: 1354

Bravo AF: 0.112

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.50

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: rs10488023; hg19: chr7-36952021;