rs1541727

chr7-37442822-A-Cchr7-37442822-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.-74+5853T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,108 control chromosomes in the GnomAD database, including 9,756 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 0.36 (9756 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

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 (AMR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.-74+5853T>G		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.-74+5853T>G		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54059 AN: 151990 Hom.: 9738 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.356 AC: 54115 AN: 152108 Hom.: 9756 Cov.: 32 AF XY: 0.349 AC XY: 25982 AN XY: 74368

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.393

Alfa AF: 0.368 Hom.: 2296

Bravo AF: 0.367

Asia WGS AF: 0.260 AC: 907 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	1.8
Dann	Benign	0.65

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: rs1541727; hg19: chr7-37482425;