Variant 20-46370389-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_133171.5(ELMO2):c.1884+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 1,520,906 control chromosomes in the GnomAD database, including 4,614 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 359 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4255 hom. )

Consequence

ELMO2
NM_133171.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.352

Variant links:

Genes affected

ELMO2 (HGNC:17233): (engulfment and cell motility 2) The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein. Similarity to a C. elegans protein suggests that this protein may function in phagocytosis of apoptotic cells and in cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ELMO2 links:

ENSG00000273828 (HGNC:):

ENSG00000273828 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 20-46370389-T-C is Benign according to our data. Variant chr20-46370389-T-C is described in ClinVar as [Benign]. Clinvar id is 1234205.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO2	NM_133171.5 linkuse as main transcript	c.1884+54A>G		intron_variant		ENST00000290246.11	NP_573403.1	Q96JJ3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELMO2	ENST00000290246.11 linkuse as main transcript	c.1884+54A>G		intron_variant		1	NM_133171.5	ENSP00000290246.6		Q96JJ3-1
ELMO2	ENST00000372176.5 linkuse as main transcript	c.1620+54A>G		intron_variant		5		ENSP00000361249.1		Q96JJ3-3

Frequencies

GnomAD3 genomes

AF:

0.0599

AC:

9118

AN:

152138

Hom.:

357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0365

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0579

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.188

Gnomad SAS

AF:

0.0893

Gnomad FIN

AF:

0.0390

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0671

Gnomad OTH

AF:

0.0655

GnomAD3 exomes

AF:

0.0714

AC:

17947

AN:

251358

Hom.:

851

AF XY:

0.0722

AC XY:

9809

AN XY:

135834

show subpopulations

Gnomad AFR exome

AF:

0.0350

Gnomad AMR exome

AF:

0.0530

Gnomad ASJ exome

AF:

0.0533

Gnomad EAS exome

AF:

0.175

Gnomad SAS exome

AF:

0.0834

Gnomad FIN exome

AF:

0.0413

Gnomad NFE exome

AF:

0.0698

Gnomad OTH exome

AF:

0.0680

GnomAD4 exome

AF:

0.0734

AC:

100419

AN:

1368650

Hom.:

4255

Cov.:

AF XY:

0.0735

AC XY:

50438

AN XY:

686220

show subpopulations

Gnomad4 AFR exome

AF:

0.0334

Gnomad4 AMR exome

AF:

0.0545

Gnomad4 ASJ exome

AF:

0.0553

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.0811

Gnomad4 FIN exome

AF:

0.0410

Gnomad4 NFE exome

AF:

0.0722

Gnomad4 OTH exome

AF:

0.0753

GnomAD4 genome

AF:

0.0599

AC:

9119

AN:

152256

Hom.:

359

Cov.:

AF XY:

0.0593

AC XY:

4416

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0365

Gnomad4 AMR

AF:

0.0578

Gnomad4 ASJ

AF:

0.0476

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.0900

Gnomad4 FIN

AF:

0.0390

Gnomad4 NFE

AF:

0.0671

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0604

Hom.:

Bravo

AF:

0.0603

Asia WGS

AF:

0.128

AC:

445

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.1

DANN

Benign

0.44

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over