rs6979467

Variant names:

• chr7-37152632-G-A
• rs6979467
• NM_014800.11:c.1087-19398C>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.1087-19398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,130 control chromosomes in the GnomAD database, including 1,268 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 0.12 (1268 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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.1087-19398C>T		intron	N/A	NP_055615.8
	ELMO1	NM_001206480.2		c.1087-19398C>T		intron	N/A	NP_001193409.1
	ELMO1	NM_001206482.2		c.1087-19398C>T		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.1087-19398C>T		intron	N/A	ENSP00000312185.4
	ELMO1	ENST00000448602.5	TSL:1	c.1087-19398C>T		intron	N/A	ENSP00000394458.1
	ELMO1	ENST00000442504.5	TSL:2	c.1087-19398C>T		intron	N/A	ENSP00000406952.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17812 AN: 152012 Hom.: 1267 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.117 AC: 17821 AN: 152130 Hom.: 1268 Cov.: 33 AF XY: 0.117 AC XY: 8668 AN XY: 74388

African (AFR) AF: 0.187 AC: 7734 AN: 41462

American (AMR) AF: 0.0766 AC: 1171 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3470

East Asian (EAS) AF: 0.102 AC: 530 AN: 5180

South Asian (SAS) AF: 0.0979 AC: 472 AN: 4820

European-Finnish (FIN) AF: 0.108 AC: 1143 AN: 10594

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.0886 AC: 6026 AN: 67992

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.0979 Hom.: 660

Bravo AF: 0.116

Asia WGS AF: 0.0990 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.67
PhyloP100		-0.46
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: rs6979467; hg19: chr7-37192237;