rs6974491

Positions:

• chr7-37334906-G-A

Variant summary

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

The NM_014800.11(ELMO1):​c.78+7707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,104 control chromosomes in the GnomAD database, including 1,492 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 (1492 hom., cov: 32)
• Consequence: ELMO1 NM_014800.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO1	NM_014800.11	c.78+7707C>T		intron_variant		ENST00000310758.9	NP_055615.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO1	ENST00000310758.9	c.78+7707C>T		intron_variant		1	NM_014800.11	ENSP00000312185	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20352 AN: 151984 Hom.: 1493 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.134 AC: 20365 AN: 152104 Hom.: 1492 Cov.: 32 AF XY: 0.131 AC XY: 9752 AN XY: 74354

Gnomad4 AFR AF: 0.0876

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.142

Alfa AF: 0.158 Hom.: 3725

Bravo AF: 0.133

Asia WGS AF: 0.0590 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.38

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: rs6974491; hg19: chr7-37374510; COSMIC: COSV60322294;