chr7-37395903-A-G

Variant names:

• chr7-37395903-A-G
• rs1882075
• NM_014800.11:c.-74+52772T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014800.11(ELMO1):​c.-74+52772T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 151,620 control chromosomes in the GnomAD database, including 69,042 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 0.95 (69042 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.-74+52772T>C		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.-74+52772T>C		intron_variant	Intron 1 of 21	1	NM_014800.11	ENSP00000312185.4

Frequencies

GnomAD3 genomes AF: 0.954 AC: 144492 AN: 151502 Hom.: 68996 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.955

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.954 AC: 144597 AN: 151620 Hom.: 69042 Cov.: 32 AF XY: 0.956 AC XY: 70889 AN XY: 74176

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.964

Gnomad4 ASJ AF: 0.955

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.969

Gnomad4 OTH AF: 0.953

Alfa AF: 0.965 Hom.: 28667

Bravo AF: 0.950

Asia WGS AF: 0.975 AC: 3387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.30
DANN	Benign	0.41

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882075; hg19: chr7-37435506;