chr7-37263990-A-G

Variant names:

• chr7-37263990-A-G
• rs2717972
• NM_014800.11:c.244-4640T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014800.11(ELMO1):​c.244-4640T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,844 control chromosomes in the GnomAD database, including 11,475 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 0.38 (11475 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 9 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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.244-4640T>C		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.244-4640T>C		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.244-4640T>C		intron	N/A	NP_001193411.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMO1	ENST00000310758.9	TSL:1 MANE Select	c.244-4640T>C		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.244-4640T>C		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.244-4640T>C		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57201 AN: 151726 Hom.: 11444 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.377 AC: 57281 AN: 151844 Hom.: 11475 Cov.: 32 AF XY: 0.379 AC XY: 28125 AN XY: 74200

African (AFR) AF: 0.518 AC: 21430 AN: 41392

American (AMR) AF: 0.384 AC: 5862 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1570 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3897 AN: 10480

Middle Eastern (MID) AF: 0.438 AC: 126 AN: 288

European-Non Finnish (NFE) AF: 0.304 AC: 20632 AN: 67922

Other (OTH) AF: 0.364 AC: 768 AN: 2108

Alfa AF: 0.337 Hom.: 11484

Bravo AF: 0.387

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2717972; hg19: chr7-37303595;