2-84446128-C-T

Position:

• chr2-84446128-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000393868.7(SUCLG1):​c.202-2728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,176 control chromosomes in the GnomAD database, including 38,001 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (38001 hom., cov: 33)
• Consequence: SUCLG1 ENST00000393868.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG1	NM_003849.4	c.202-2728G>A		intron_variant		ENST00000393868.7	NP_003840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7	c.202-2728G>A		intron_variant		1	NM_003849.4	ENSP00000377446	P1

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103904 AN: 152056 Hom.: 37991 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.709

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.683 AC: 103942 AN: 152176 Hom.: 38001 Cov.: 33 AF XY: 0.690 AC XY: 51326 AN XY: 74428

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.707

Alfa AF: 0.769 Hom.: 60183

Bravo AF: 0.668

Asia WGS AF: 0.814 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs10210248; hg19: chr2-84673252;