chr7-36875580-T-C

Variant names:

• chr7-36875580-T-C
• rs1558688
• NM_014800.11:c.1822+2430A>G

Variant summary

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

The NM_014800.11(ELMO1):​c.1822+2430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,066 control chromosomes in the GnomAD database, including 29,725 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 0.62 (29725 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.1822+2430A>G		intron_variant	Intron 19 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.1822+2430A>G		intron_variant	Intron 19 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93842 AN: 151948 Hom.: 29706 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.618 AC: 93903 AN: 152066 Hom.: 29725 Cov.: 32 AF XY: 0.617 AC XY: 45885 AN XY: 74334

African (AFR) AF: 0.475 AC: 19687 AN: 41462

American (AMR) AF: 0.577 AC: 8823 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2260 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3517 AN: 5168

South Asian (SAS) AF: 0.664 AC: 3204 AN: 4826

European-Finnish (FIN) AF: 0.695 AC: 7360 AN: 10584

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47017 AN: 67958

Other (OTH) AF: 0.613 AC: 1292 AN: 2106

Alfa AF: 0.661 Hom.: 31887

Bravo AF: 0.604

Asia WGS AF: 0.630 AC: 2188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.48
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: rs1558688; hg19: chr7-36915185;