rs2160430

Positions:

• chr7-37183796-T-C
• chr7-37183796-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014800.11(ELMO1):​c.1086+27590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,000 control chromosomes in the GnomAD database, including 41,832 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 0.74 (41832 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1086+27590A>G		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1086+27590A>G		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112428 AN: 151882 Hom.: 41814 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.740 AC: 112492 AN: 152000 Hom.: 41832 Cov.: 31 AF XY: 0.744 AC XY: 55259 AN XY: 74268

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.729

Alfa AF: 0.754 Hom.: 71912

Bravo AF: 0.732

Asia WGS AF: 0.800 AC: 2782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.75

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: rs2160430; hg19: chr7-37223401;