rs1345365

Positions:

• chr7-37161008-G-A
• chr7-37161008-G-T

Variant summary

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

The NM_014800.11(ELMO1):​c.1087-27774C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 151,990 control chromosomes in the GnomAD database, including 31,297 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 0.62 (31297 hom., cov: 31)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.1087-27774C>T		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.1087-27774C>T		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93996 AN: 151872 Hom.: 31303 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.619 AC: 94009 AN: 151990 Hom.: 31297 Cov.: 31 AF XY: 0.623 AC XY: 46254 AN XY: 74296

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.636

Alfa AF: 0.714 Hom.: 51637

Bravo AF: 0.602

Asia WGS AF: 0.629 AC: 2188 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	0.023
DANN	Benign	0.86

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: rs1345365; hg19: chr7-37200613;