2-84449762-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAA

Position:

• chr2-84449762-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_003849.4(SUCLG1):​c.98-11_98-10insTT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000011 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000063 (0 hom.)
• Consequence: SUCLG1 NM_003849.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG1	NM_003849.4	c.98-11_98-10insTT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000393868.7	NP_003840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7	c.98-11_98-10insTT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003849.4	ENSP00000377446	P1

Frequencies

GnomAD3 genomes AF: 0.0000111 AC: 1 AN: 90116 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000120

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000627 AC: 44 AN: 701926 Hom.: 0 Cov.: 0 AF XY: 0.0000575 AC XY: 21 AN XY: 365294

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000508

Gnomad4 ASJ exome AF: 0.000123

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000847

Gnomad4 FIN exome AF: 0.0000252

Gnomad4 NFE exome AF: 0.0000641

Gnomad4 OTH exome AF: 0.000125

GnomAD4 genome AF: 0.0000111 AC: 1 AN: 90116 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 41562

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000120

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs56733272; hg19: chr2-84676886;