rs9969311

Positions:

• chr7-37375454-G-A
• chr7-37375454-G-C
• chr7-37375454-G-T

Variant summary

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

The NM_014800.11(ELMO1):​c.-73-32691C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 655,996 control chromosomes in the GnomAD database, including 16,901 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 0.18 (3011 hom., cov: 32)
  • Exomes 𝑓: 0.19 (13890 hom.)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.-73-32691C>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.-73-32691C>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26750 AN: 151964 Hom.: 3003 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.193 AC: 97131 AN: 503914 Hom.: 13890 AF XY: 0.197 AC XY: 52988 AN XY: 268924

Gnomad4 AFR exome AF: 0.174

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.605

Gnomad4 SAS exome AF: 0.305

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.178

GnomAD4 genome AF: 0.176 AC: 26788 AN: 152082 Hom.: 3011 Cov.: 32 AF XY: 0.185 AC XY: 13742 AN XY: 74328

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.189

Alfa AF: 0.0958 Hom.: 199

Bravo AF: 0.185

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.56

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: rs9969311; hg19: chr7-37415057;