rs7785934

chr7-36861974-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.1906-238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 535,124 control chromosomes in the GnomAD database, including 51,111 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 0.41 (13480 hom., cov: 31)
  • Exomes 𝑓: 0.44 (37631 hom.)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1906-238A>G		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1906-238A>G		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62871 AN: 151832 Hom.: 13474 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.438 AC: 167777 AN: 383174 Hom.: 37631 Cov.: 3 AF XY: 0.434 AC XY: 87514 AN XY: 201538

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.344

Gnomad4 ASJ exome AF: 0.394

Gnomad4 EAS exome AF: 0.331

Gnomad4 SAS exome AF: 0.370

Gnomad4 FIN exome AF: 0.482

Gnomad4 NFE exome AF: 0.474

Gnomad4 OTH exome AF: 0.424

GnomAD4 genome AF: 0.414 AC: 62885 AN: 151950 Hom.: 13480 Cov.: 31 AF XY: 0.412 AC XY: 30566 AN XY: 74248

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.389

Alfa AF: 0.454 Hom.: 15706

Bravo AF: 0.400

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.8
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: rs7785934; hg19: chr7-36901579;