2-84449762-TAAAAAAAAAAAAAAA-TAAAAAA

Position:

• chr2-84449762-TAAAAAAAAAAAAAAA-TAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_003849.4(SUCLG1):​c.98-19_98-11delTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000689 in 701,166 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.00069 (0 hom.)
• Consequence: SUCLG1 NM_003849.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

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 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.000689 (483/701166) while in subpopulation AFR AF= 0.0009 (14/15558). AF 95% confidence interval is 0.000606. There are 0 homozygotes in gnomad4_exome. There are 257 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG1	NM_003849.4	c.98-19_98-11delTTTTTTTTT		intron_variant		ENST00000393868.7	NP_003840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7	c.98-19_98-11delTTTTTTTTT		intron_variant		1	NM_003849.4	ENSP00000377446.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.000689 AC: 483 AN: 701166 Hom.: 0 AF XY: 0.000704 AC XY: 257 AN XY: 364912

Gnomad4 AFR exome AF: 0.000900

Gnomad4 AMR exome AF: 0.000662

Gnomad4 ASJ exome AF: 0.00111

Gnomad4 EAS exome AF: 0.000845

Gnomad4 SAS exome AF: 0.000678

Gnomad4 FIN exome AF: 0.000353

Gnomad4 NFE exome AF: 0.000665

Gnomad4 OTH exome AF: 0.00103

GnomAD4 genome Cov.: 0

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;