rs7804092

chr7-36853627-T-A

Variant summary

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

The NM_014800.11(ELMO1):c.*1924A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,176 control chromosomes in the GnomAD database, including 2,570 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 0.18 (2570 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.*1924A>T		3_prime_UTR_variant	22/22	ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.*1924A>T		3_prime_UTR_variant	22/22	1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27285 AN: 152058 Hom.: 2563 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.179 AC: 27311 AN: 152176 Hom.: 2570 Cov.: 32 AF XY: 0.185 AC XY: 13738 AN XY: 74404

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.177

Alfa AF: 0.174 Hom.: 296

Bravo AF: 0.175

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.1
Dann	Benign	0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7804092; hg19: chr7-36893232;