7-37147952-T-G

Variant summary

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

The NM_014800.11(ELMO1):c.1087-14718A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,114 control chromosomes in the GnomAD database, including 53,948 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 0.84 (53948 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

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 = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1087-14718A>C		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1087-14718A>C		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127116 AN: 151996 Hom.: 53930 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.836 AC: 127183 AN: 152114 Hom.: 53948 Cov.: 31 AF XY: 0.840 AC XY: 62449 AN XY: 74360

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.839

Alfa AF: 0.880 Hom.: 9462

Bravo AF: 0.821

Asia WGS AF: 0.821 AC: 2857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.4
Dann	Benign	0.63

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: rs6462731; hg19: chr7-37187557;