Variant 20-46369117-G-A 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.1885-149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 682,582 control chromosomes in the GnomAD database, including 6,055 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1118 hom., cov: 32)

Exomes 𝑓: 0.13 ( 4937 hom. )

Consequence

ELMO2
NM_133171.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.10

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=-0.68).

BP6

Variant 20-46369117-G-A is Benign according to our data. Variant chr20-46369117-G-A is described in ClinVar as [Benign]. Clinvar id is 1246786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELMO2	NM_133171.5 link	c.1885-149C>T		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 link	c.1885-149C>T		intron_variant		1	NM_133171.5	ENSP00000290246.6		Q96JJ3-1
ELMO2	ENST00000372176.5 link	c.1621-149C>T		intron_variant		5		ENSP00000361249.1		Q96JJ3-3

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16560

AN:

152124

Hom.:

1118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0450

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.0815

Gnomad SAS

AF:

0.0935

Gnomad FIN

AF:

0.0717

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.123

GnomAD4 exome

AF:

0.130

AC:

68696

AN:

530340

Hom.:

4937

Cov.:

AF XY:

0.129

AC XY:

36088

AN XY:

279306

show subpopulations

Gnomad4 AFR exome

AF:

0.0460

Gnomad4 AMR exome

AF:

0.154

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.0771

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.0751

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.138

GnomAD4 genome

AF:

0.109

AC:

16565

AN:

152242

Hom.:

1118

Cov.:

AF XY:

0.106

AC XY:

7882

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.0448

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.216

Gnomad4 EAS

AF:

0.0815

Gnomad4 SAS

AF:

0.0949

Gnomad4 FIN

AF:

0.0717

Gnomad4 NFE

AF:

0.144

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.113

Hom.:

167

Bravo

AF:

0.114

Asia WGS

AF:

0.0870

AC:

304

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 11, 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

-0.68

CADD

Benign

8.5

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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