7-37358670-C-T

Variant names:

• chr7-37358670-C-T
• rs17259795
• NM_014800.11:c.-73-15907G>A

Variant summary

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

The NM_014800.11(ELMO1):​c.-73-15907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,008 control chromosomes in the GnomAD database, including 2,912 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 0.19 (2912 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.-73-15907G>A		intron_variant	Intron 1 of 21	ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.-73-15907G>A		intron_variant	Intron 1 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28415 AN: 151890 Hom.: 2913 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.187 AC: 28425 AN: 152008 Hom.: 2912 Cov.: 32 AF XY: 0.188 AC XY: 13939 AN XY: 74296

African (AFR) AF: 0.123 AC: 5099 AN: 41464

American (AMR) AF: 0.198 AC: 3029 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 567 AN: 3464

East Asian (EAS) AF: 0.0211 AC: 109 AN: 5172

South Asian (SAS) AF: 0.170 AC: 820 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2480 AN: 10538

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15693 AN: 67968

Other (OTH) AF: 0.204 AC: 430 AN: 2106

Alfa AF: 0.217 Hom.: 2672

Bravo AF: 0.178

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.19
PhyloP100		0.063
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: rs17259795; hg19: chr7-37398273;