Variant chr20-46371783-G-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.1580+23C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0868 in 1,613,734 control chromosomes in the GnomAD database, including 8,376 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 2132 hom., cov: 32)

Exomes 𝑓: 0.082 ( 6244 hom. )

Consequence

ELMO2
NM_133171.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.791

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:

ELMO2 (HGNC:):

ELMO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 20-46371783-G-C is Benign according to our data. Variant chr20-46371783-G-C is described in ClinVar as [Benign]. Clinvar id is 1279359.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 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.1580+23C>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.1580+23C>G		intron_variant		1	NM_133171.5	ENSP00000290246.6		Q96JJ3-1
ELMO2	ENST00000372176.5 linkuse as main transcript	c.1316+23C>G		intron_variant		5		ENSP00000361249.1		Q96JJ3-3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20406

AN:

152072

Hom.:

2123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0916

Gnomad ASJ

AF:

0.0536

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0903

Gnomad FIN

AF:

0.0387

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0685

Gnomad OTH

AF:

0.125

GnomAD3 exomes

AF:

0.0915

AC:

22985

AN:

251080

Hom.:

1592

AF XY:

0.0873

AC XY:

11848

AN XY:

135696

show subpopulations

Gnomad AFR exome

AF:

0.297

Gnomad AMR exome

AF:

0.0678

Gnomad ASJ exome

AF:

0.0585

Gnomad EAS exome

AF:

0.174

Gnomad SAS exome

AF:

0.0839

Gnomad FIN exome

AF:

0.0413

Gnomad NFE exome

AF:

0.0711

Gnomad OTH exome

AF:

0.0800

GnomAD4 exome

AF:

0.0819

AC:

119635

AN:

1461544

Hom.:

6244

Cov.:

AF XY:

0.0808

AC XY:

58778

AN XY:

727022

show subpopulations

Gnomad4 AFR exome

AF:

0.299

Gnomad4 AMR exome

AF:

0.0717

Gnomad4 ASJ exome

AF:

0.0600

Gnomad4 EAS exome

AF:

0.194

Gnomad4 SAS exome

AF:

0.0818

Gnomad4 FIN exome

AF:

0.0410

Gnomad4 NFE exome

AF:

0.0735

Gnomad4 OTH exome

AF:

0.0948

GnomAD4 genome

AF:

0.134

AC:

20447

AN:

152190

Hom.:

2132

Cov.:

AF XY:

0.130

AC XY:

9674

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.0914

Gnomad4 ASJ

AF:

0.0536

Gnomad4 EAS

AF:

0.186

Gnomad4 SAS

AF:

0.0908

Gnomad4 FIN

AF:

0.0387

Gnomad4 NFE

AF:

0.0685

Gnomad4 OTH

AF:

0.124

Alfa

AF:

0.0920

Hom.:

211

Bravo

AF:

0.145

Asia WGS

AF:

0.145

AC:

503

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.069

DANN

Benign

0.63

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