rs1882080

Positions:

• chr7-36916236-G-A
• chr7-36916236-G-C

Variant summary

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

The NM_014800.11(ELMO1):​c.1438-21219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,912 control chromosomes in the GnomAD database, including 17,302 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 0.46 (17302 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1438-21219C>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1438-21219C>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69424 AN: 151794 Hom.: 17301 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.457 AC: 69434 AN: 151912 Hom.: 17302 Cov.: 31 AF XY: 0.457 AC XY: 33970 AN XY: 74252

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.445

Alfa AF: 0.430 Hom.: 2369

Bravo AF: 0.433

Asia WGS AF: 0.345 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.58

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: rs1882080; hg19: chr7-36955841;