rs7804092

Variant names:

• chr7-36853627-T-A
• rs7804092
• NM_014800.11:c.*1924A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ELMO1 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014800.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	NM_014800.11	MANE Select	c.*1924A>T		3_prime_UTR	Exon 22 of 22	NP_055615.8
	ELMO1	NM_001206480.2		c.*1924A>T		3_prime_UTR	Exon 22 of 22	NP_001193409.1
	ELMO1	NM_001206482.2		c.*1924A>T		3_prime_UTR	Exon 22 of 22	NP_001193411.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.*1924A>T		3_prime_UTR	Exon 22 of 22	ENSP00000312185.4

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

African (AFR) AF: 0.165 AC: 6864 AN: 41522

American (AMR) AF: 0.230 AC: 3512 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 630 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1195 AN: 5168

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4830

European-Finnish (FIN) AF: 0.239 AC: 2535 AN: 10588

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10807 AN: 67980

Other (OTH) AF: 0.177 AC: 374 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.20
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs7804092; hg19: chr7-36893232;