3-67529111-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_003848.4(SUCLG2):c.302A>G(p.Lys101Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00778 in 1,612,796 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0048 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 66 hom. )

Consequence

SUCLG2
NM_003848.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 7.99

Publications

12 publications found

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 was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.019182414).

BP6

Variant 3-67529111-T-C is Benign according to our data. Variant chr3-67529111-T-C is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 257601.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG2	NM_003848.4 link	c.302A>G	p.Lys101Arg	missense_variant	Exon 3 of 11	ENST00000307227.10	NP_003839.2	Q96I99-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SUCLG2	ENST00000307227.10 link	c.302A>G	p.Lys101Arg	missense_variant	Exon 3 of 11	1	NM_003848.4	ENSP00000307432.5	Q96I99-1
SUCLG2	ENST00000493112.5 link	c.302A>G	p.Lys101Arg	missense_variant	Exon 3 of 11	1		ENSP00000419325.1	Q96I99-2
SUCLG2	ENST00000492795.1 link	c.302A>G	p.Lys101Arg	missense_variant	Exon 3 of 10	2		ENSP00000417589.1	E9PDQ8

Frequencies

GnomAD3 genomes

AF:

0.00482

AC:

733

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00923

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.000848

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00861

Gnomad OTH

AF:

0.00526

GnomAD2 exomes

AF:

0.00482

AC:

1198

AN:

248596

AF XY:

0.00497

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00172

Gnomad ASJ exome

AF:

0.00777

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00149

Gnomad NFE exome

AF:

0.00797

Gnomad OTH exome

AF:

0.00514

GnomAD4 exome

AF:

0.00809

AC:

11820

AN:

1460550

Hom.:

Cov.:

AF XY:

0.00788

AC XY:

5726

AN XY:

726532

show subpopulations

African (AFR)

AF:

0.00111

AC:

AN:

33416

American (AMR)

AF:

0.00152

AC:

AN:

44612

Ashkenazi Jewish (ASJ)

AF:

0.00697

AC:

182

AN:

26112

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39682

South Asian (SAS)

AF:

0.00238

AC:

205

AN:

85992

European-Finnish (FIN)

AF:

0.00195

AC:

104

AN:

53410

Middle Eastern (MID)

AF:

0.00150

AC:

AN:

5334

European-Non Finnish (NFE)

AF:

0.00970

AC:

10781

AN:

1111666

Other (OTH)

AF:

0.00719

AC:

434

AN:

60326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

516

1032

1547

2063

2579

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

430

860

1290

1720

2150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00481

AC:

733

AN:

152246

Hom.:

Cov.:

AF XY:

0.00390

AC XY:

290

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.00156

AC:

AN:

41550

American (AMR)

AF:

0.00170

AC:

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.00923

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5174

South Asian (SAS)

AF:

0.000829

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000848

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00862

AC:

586

AN:

68016

Other (OTH)

AF:

0.00520

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

118

157

196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00741

Hom.:

Bravo

AF:

0.00489

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00163

AC:

ESP6500EA

AF:

0.0105

AC:

ExAC

AF:

0.00475

AC:

574

Asia WGS

AF:

0.00144

AC:

AN:

3476

EpiCase

AF:

0.00857

EpiControl

AF:

0.00968

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.16

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.35

.;T;.

Eigen

Uncertain

0.33

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

D;D;D

MetaRNN

Benign

0.019

T;T;T

MetaSVM

Uncertain

-0.20

MutationAssessor

Uncertain

2.4

M;M;.

PhyloP100

8.0

PrimateAI

Uncertain

0.57

PROVEAN

Benign

-2.1

N;N;N

REVEL

Uncertain

0.46

Sift

Benign

0.034

D;D;D

Sift4G

Uncertain

0.025

D;D;D

Polyphen

0.14

.;B;.

Vest4

0.56

MVP

0.73

MPC

0.075

ClinPred

0.050

GERP RS

5.0

Varity_R

0.40

gMVP

0.62

Mutation Taster

=94/6

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over