Variant rs150352166 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_003848.4(SUCLG2):c.758-10_758-8del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 1,612,360 control chromosomes in the GnomAD database, including 9,121 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1686 hom., cov: 31)

Exomes 𝑓: 0.078 ( 7435 hom. )

Consequence

SUCLG2
NM_003848.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 2.25

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-67498302-AAAG-A is Benign according to our data. Variant chr3-67498302-AAAG-A is described in ClinVar as [Benign]. Clinvar id is 257602.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUCLG2	NM_003848.4 linkuse as main transcript	c.758-10_758-8del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000307227.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
SUCLG2	ENST00000307227.10 linkuse as main transcript	c.758-10_758-8del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_003848.4	P1	Q96I99-1
SUCLG2	ENST00000460567.5 linkuse as main transcript	c.334+19942_334+19944del	intron_variant	1
SUCLG2	ENST00000493112.5 linkuse as main transcript	c.758-10_758-8del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1			Q96I99-2
SUCLG2	ENST00000492795.1 linkuse as main transcript	c.758-10_758-8del	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18742

AN:

152032

Hom.:

1683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.152

Gnomad ASJ

AF:

0.0761

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.0543

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0546

Gnomad OTH

AF:

0.109

GnomAD3 exomes

AF:

0.121

AC:

30052

AN:

247344

Hom.:

2887

AF XY:

0.116

AC XY:

15513

AN XY:

134256

show subpopulations

Gnomad AFR exome

AF:

0.224

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.0708

Gnomad EAS exome

AF:

0.307

Gnomad SAS exome

AF:

0.165

Gnomad FIN exome

AF:

0.0511

Gnomad NFE exome

AF:

0.0535

Gnomad OTH exome

AF:

0.0883

GnomAD4 exome

AF:

0.0781

AC:

114021

AN:

1460210

Hom.:

7435

AF XY:

0.0794

AC XY:

57667

AN XY:

726382

show subpopulations

Gnomad4 AFR exome

AF:

0.226

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.0748

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.0528

Gnomad4 NFE exome

AF:

0.0541

Gnomad4 OTH exome

AF:

0.0874

GnomAD4 genome

AF:

0.123

AC:

18771

AN:

152150

Hom.:

1686

Cov.:

AF XY:

0.127

AC XY:

9465

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.221

Gnomad4 AMR

AF:

0.152

Gnomad4 ASJ

AF:

0.0761

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.0543

Gnomad4 NFE

AF:

0.0545

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.0835

Hom.:

142

Bravo

AF:

0.138

Asia WGS

AF:

0.245

AC:

853

AN:

3476

EpiCase

AF:

0.0547

EpiControl

AF:

0.0521

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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