Variant 2-84449762-TAAAAAAAAAAAAAAA-TAAAAAAAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003849.4(SUCLG1):c.98-16_98-11delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 773,678 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 0)

Exomes 𝑓: 0.056 ( 6 hom. )

Consequence

SUCLG1
NM_003849.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.74

Variant links:

Genes affected

SUCLG1 (HGNC:11449): (succinate-CoA ligase GDP/ADP-forming subunit alpha) This gene encodes the alpha subunit of the heterodimeric enzyme succinate coenzyme A ligase. This enzyme is targeted to the mitochondria and catalyzes the conversion of succinyl CoA and ADP or GDP to succinate and ATP or GTP. Mutations in this gene are the cause of the metabolic disorder fatal infantile lactic acidosis and mitochondrial DNA depletion. [provided by RefSeq, Feb 2010]

SUCLG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG1	NM_003849.4 link	c.98-16_98-11delTTTTTT		intron_variant	Intron 1 of 8	ENST00000393868.7	NP_003840.2	P53597

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7 link	c.98-16_98-11delTTTTTT		intron_variant	Intron 1 of 8	1	NM_003849.4	ENSP00000377446.2		P53597

Frequencies

GnomAD3 genomes

AF:

0.00141

AC:

127

AN:

90114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00440

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000838

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000336

Gnomad SAS

AF:

0.00128

Gnomad FIN

AF:

0.000382

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000675

Gnomad OTH

AF:

0.00172

GnomAD4 exome

AF:

0.0555

AC:

37959

AN:

683558

Hom.:

AF XY:

0.0552

AC XY:

19606

AN XY:

355064

show subpopulations

Gnomad4 AFR exome

AF:

0.0835

Gnomad4 AMR exome

AF:

0.0636

Gnomad4 ASJ exome

AF:

0.0644

Gnomad4 EAS exome

AF:

0.0658

Gnomad4 SAS exome

AF:

0.0566

Gnomad4 FIN exome

AF:

0.0408

Gnomad4 NFE exome

AF:

0.0540

Gnomad4 OTH exome

AF:

0.0629

GnomAD4 genome

AF:

0.00142

AC:

128

AN:

90120

Hom.:

Cov.:

AF XY:

0.00135

AC XY:

AN XY:

41572

show subpopulations

Gnomad4 AFR

AF:

0.00444

Gnomad4 AMR

AF:

0.000837

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000337

Gnomad4 SAS

AF:

0.00129

Gnomad4 FIN

AF:

0.000382

Gnomad4 NFE

AF:

0.0000675

Gnomad4 OTH

AF:

0.00170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over