rs2700987

chr7-37346633-C-Achr7-37346633-C-G

Variant summary

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

The NM_014800.11(ELMO1):c.-73-3870G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,138 control chromosomes in the GnomAD database, including 28,095 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 0.60 (28095 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.-73-3870G>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.-73-3870G>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91664 AN: 152020 Hom.: 28058 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.603 AC: 91746 AN: 152138 Hom.: 28095 Cov.: 33 AF XY: 0.611 AC XY: 45459 AN XY: 74372

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.640

Alfa AF: 0.580 Hom.: 5699

Bravo AF: 0.609

Asia WGS AF: 0.755 AC: 2626 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.7
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2700987; hg19: chr7-37386237;