rs2041801

chr7-36887236-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.1714+324C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,034 control chromosomes in the GnomAD database, including 17,311 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 0.46 (17311 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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]

LOC105375235 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1714+324C>T		intron_variant		ENST00000310758.9
LOC105375235	XR_007060290.1	n.2785+2449G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1714+324C>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69252 AN: 151916 Hom.: 17309 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.456 AC: 69261 AN: 152034 Hom.: 17311 Cov.: 32 AF XY: 0.456 AC XY: 33873 AN XY: 74308

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.445

Alfa AF: 0.533 Hom.: 37849

Bravo AF: 0.432

Asia WGS AF: 0.350 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.59
Dann	Benign	0.50

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: rs2041801; hg19: chr7-36926841; COSMIC: COSV60302557;