rs2717972

Positions:

• chr7-37263990-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.244-4640T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,844 control chromosomes in the GnomAD database, including 11,475 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 0.38 (11475 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.244-4640T>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.244-4640T>C		intron_variant		1	NM_014800.11	ENSP00000312185	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57201 AN: 151726 Hom.: 11444 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.377 AC: 57281 AN: 151844 Hom.: 11475 Cov.: 32 AF XY: 0.379 AC XY: 28125 AN XY: 74200

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.364

Alfa AF: 0.328 Hom.: 8275

Bravo AF: 0.387

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.68

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: rs2717972; hg19: chr7-37303595;