rs741301

Positions:

• chr7-36878390-C-T

Variant summary

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

The NM_014800.11(ELMO1):​c.1715-273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,862 control chromosomes in the GnomAD database, including 27,490 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 0.59 (27490 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

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 = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1715-273G>A		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1715-273G>A		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89690 AN: 151742 Hom.: 27471 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.591 AC: 89736 AN: 151862 Hom.: 27490 Cov.: 31 AF XY: 0.592 AC XY: 43917 AN XY: 74228

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.597

Alfa AF: 0.651 Hom.: 55605

Bravo AF: 0.576

Asia WGS AF: 0.603 AC: 2097 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	0.31
DANN	Benign	0.42

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: rs741301; hg19: chr7-36917995;