7-37226747-T-C

Position:

• chr7-37226747-T-C

Variant summary

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

The NM_014800.11(ELMO1):​c.550-1717A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0677 in 152,208 control chromosomes in the GnomAD database, including 650 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 0.068 (650 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.550-1717A>G		intron_variant		ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.550-1717A>G		intron_variant		1	NM_014800.11	ENSP00000312185	P1
ELMO1	ENST00000448602.5	c.550-1717A>G		intron_variant		1		ENSP00000394458	P1
ELMO1	ENST00000442504.5	c.550-1717A>G		intron_variant		2		ENSP00000406952	P1

Frequencies

GnomAD3 genomes AF: 0.0676 AC: 10280 AN: 152088 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0677 AC: 10309 AN: 152208 Hom.: 650 Cov.: 32 AF XY: 0.0707 AC XY: 5259 AN XY: 74418

Gnomad4 AFR AF: 0.0860

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.0398

Gnomad4 NFE AF: 0.0282

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0437 Hom.: 410

Bravo AF: 0.0812

Asia WGS AF: 0.157 AC: 542 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.64

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: rs4723619; hg19: chr7-37266352;