7-36889359-C-T

Variant summary

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

The NM_014800.11(ELMO1):c.1602-1687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,084 control chromosomes in the GnomAD database, including 42,586 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 0.74 (42586 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1602-1687G>A		intron_variant		ENST00000310758.9
LOC105375235	XR_007060290.1	n.2786-828C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1602-1687G>A		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113163 AN: 151966 Hom.: 42566 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.744 AC: 113220 AN: 152084 Hom.: 42586 Cov.: 31 AF XY: 0.740 AC XY: 55013 AN XY: 74352

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.741

Alfa AF: 0.793 Hom.: 62379

Bravo AF: 0.735

Asia WGS AF: 0.706 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.70
Dann	Benign	0.46

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: rs7799004; hg19: chr7-36928964;