rs6949576

chr7-36865715-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.1906-3979T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,096 control chromosomes in the GnomAD database, including 22,506 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 0.54 (22506 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1906-3979T>C		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1906-3979T>C		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82189 AN: 151978 Hom.: 22483 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.541 AC: 82248 AN: 152096 Hom.: 22506 Cov.: 32 AF XY: 0.543 AC XY: 40381 AN XY: 74364

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.514

Alfa AF: 0.557 Hom.: 22976

Bravo AF: 0.530

Asia WGS AF: 0.553 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.5
Dann	Benign	0.78

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: rs6949576; hg19: chr7-36905320;