rs13225050

Positions:

• chr7-37173503-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.1086+37883C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0734 in 152,324 control chromosomes in the GnomAD database, including 463 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 0.073 (463 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1086+37883C>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1086+37883C>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.0735 AC: 11183 AN: 152206 Hom.: 464 Cov.: 33

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0734 AC: 11181 AN: 152324 Hom.: 463 Cov.: 33 AF XY: 0.0739 AC XY: 5501 AN XY: 74476

Gnomad4 AFR AF: 0.0973

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0673 Hom.: 345

Bravo AF: 0.0697

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.84

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: rs13225050; hg19: chr7-37213108;