rs6979467

Positions:

• chr7-37152632-G-A

Variant summary

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

The NM_014800.11(ELMO1):​c.1087-19398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,130 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1087-19398C>T		intron_variant		ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1087-19398C>T		intron_variant		1	NM_014800.11	ENSP00000312185	P1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17812 AN: 152012 Hom.: 1267 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.117 AC: 17821 AN: 152130 Hom.: 1268 Cov.: 33 AF XY: 0.117 AC XY: 8668 AN XY: 74388

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0979 Hom.: 503

Bravo AF: 0.116

Asia WGS AF: 0.0990 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.67

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: rs6979467; hg19: chr7-37192237;