rs6956864

chr7-37264145-T-C

Variant summary

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

The NM_014800.11(ELMO1):c.244-4795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0456 in 152,188 control chromosomes in the GnomAD database, including 331 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 0.046 (331 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.244-4795A>G		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.244-4795A>G		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6918 AN: 152070 Hom.: 324 Cov.: 32

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0456 AC: 6934 AN: 152188 Hom.: 331 Cov.: 32 AF XY: 0.0493 AC XY: 3666 AN XY: 74416

Gnomad4 AFR AF: 0.0101

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.0840

Gnomad4 FIN AF: 0.0439

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0403 Hom.: 76

Bravo AF: 0.0500

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.8
Dann	Benign	0.41

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: rs6956864; hg19: chr7-37303750;