chr7-37397251-A-G

Position:

• chr7-37397251-A-G

Variant summary

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

The NM_014800.11(ELMO1):​c.-74+51424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,266 control chromosomes in the GnomAD database, including 1,588 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 0.13 (1588 hom., cov: 33)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ELMO1	NM_014800.11	c.-74+51424T>C		intron_variant		ENST00000310758.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELMO1	ENST00000310758.9	c.-74+51424T>C		intron_variant		1	NM_014800.11	P1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19985 AN: 152148 Hom.: 1587 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.131 AC: 19991 AN: 152266 Hom.: 1588 Cov.: 33 AF XY: 0.130 AC XY: 9695 AN XY: 74464

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0645

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.0826

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.137

Alfa AF: 0.109 Hom.: 1051

Bravo AF: 0.133

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.77

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: rs11984075; hg19: chr7-37436854;