rs10242920

Positions:

• chr7-37329953-C-A
• chr7-37329953-C-G
• chr7-37329953-C-T

Variant summary

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

The NM_014800.11(ELMO1):​c.78+12660G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,042 control chromosomes in the GnomAD database, including 4,116 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 0.23 (4116 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

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 (SAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.78+12660G>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.78+12660G>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35448 AN: 151924 Hom.: 4112 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.233 AC: 35483 AN: 152042 Hom.: 4116 Cov.: 32 AF XY: 0.231 AC XY: 17200 AN XY: 74326

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.250

Alfa AF: 0.234 Hom.: 8692

Bravo AF: 0.233

Asia WGS AF: 0.254 AC: 883 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	1.2
DANN	Benign	0.60

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: rs10242920; hg19: chr7-37369557;