rs6942726

Positions:

• chr7-36918303-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.1438-23286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,096 control chromosomes in the GnomAD database, including 5,264 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 0.26 (5264 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

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]

ELMO1 (HGNC:):

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 = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1438-23286A>G		intron_variant		ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1438-23286A>G		intron_variant		1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39351 AN: 151978 Hom.: 5256 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.259 AC: 39385 AN: 152096 Hom.: 5264 Cov.: 32 AF XY: 0.259 AC XY: 19251 AN XY: 74340

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.254

Alfa AF: 0.276 Hom.: 5736

Bravo AF: 0.256

Asia WGS AF: 0.288 AC: 1002 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	0.063
DANN	Benign	0.75

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: rs6942726; hg19: chr7-36957908;