Variant rs902320 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 ENST00000493112.5(SUCLG2):c.1273G>A(p.Val425Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,519,890 control chromosomes in the GnomAD database, including 51,862 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4700 hom., cov: 33)

Exomes 𝑓: 0.26 ( 47162 hom. )

Consequence

SUCLG2
ENST00000493112.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.00600

Variant links:

Genes affected

SUCLG2 (HGNC:11450): (succinate-CoA ligase GDP-forming subunit beta) This gene encodes a GTP-specific beta subunit of succinyl-CoA synthetase. Succinyl-CoA synthetase catalyzes the reversible reaction involving the formation of succinyl-CoA and succinate. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 5 and 12. [provided by RefSeq, Apr 2010]

SUCLG2 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 (MetaRNN=0.002345711).

BP6

Variant 3-67360679-C-T is Benign according to our data. Variant chr3-67360679-C-T is described in ClinVar as [Benign]. Clinvar id is 257600.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG2	NM_001177599.2 linkuse as main transcript	c.1273G>A	p.Val425Ile	missense_variant	11/11		NP_001171070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG2	ENST00000493112.5 linkuse as main transcript	c.1273G>A	p.Val425Ile	missense_variant	11/11	1		ENSP00000419325		Q96I99-2

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37282

AN:

151952

Hom.:

4692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.241

AC:

31757

AN:

131920

Hom.:

4157

AF XY:

0.239

AC XY:

17194

AN XY:

71876

show subpopulations

Gnomad AFR exome

AF:

0.188

Gnomad AMR exome

AF:

0.232

Gnomad ASJ exome

AF:

0.140

Gnomad EAS exome

AF:

0.260

Gnomad SAS exome

AF:

0.224

Gnomad FIN exome

AF:

0.353

Gnomad NFE exome

AF:

0.261

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.259

AC:

354489

AN:

1367820

Hom.:

47162

Cov.:

AF XY:

0.257

AC XY:

173547

AN XY:

674468

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.145

Gnomad4 EAS exome

AF:

0.261

Gnomad4 SAS exome

AF:

0.226

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.266

Gnomad4 OTH exome

AF:

0.241

GnomAD4 genome

AF:

0.245

AC:

37319

AN:

152070

Hom.:

4700

Cov.:

AF XY:

0.246

AC XY:

18285

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.203

Gnomad4 AMR

AF:

0.200

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.234

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.211

Alfa

AF:

0.255

Hom.:

8054

Bravo

AF:

0.233

TwinsUK

AF:

0.270

AC:

1003

ALSPAC

AF:

0.268

AC:

1031

ExAC

AF:

0.195

AC:

2866

Asia WGS

AF:

0.275

AC:

958

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.1

DANN

Benign

0.21

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.83

FATHMM_MKL

Benign

0.060

LIST_S2

Benign

0.34

MetaRNN

Benign

0.0023

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

PROVEAN

Benign

-0.28

REVEL

Benign

0.035

Sift

Uncertain

0.025

Sift4G

Benign

0.18

Vest4

0.028

MPC

0.053

ClinPred

0.012

GERP RS

1.6

gMVP

0.59

Splicing

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