ENST00000643584.1:n.*214+16341G>T

Variant names:

• chr13-47888988-C-A
• rs7986369
• ENST00000643584.1:n.*214+16341G>T

Variant summary

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

The ENST00000643584.1(SUCLA2):​n.*214+16341G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,018 control chromosomes in the GnomAD database, including 12,516 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 0.40 (12516 hom., cov: 32)
• Consequence: SUCLA2 ENST00000643584.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

SUCLA2 (HGNC:11448): (succinate-CoA ligase ADP-forming subunit beta) Succinyl-CoA synthetase (SCS) is a mitochondrial matrix enzyme that acts as a heterodimer, being composed of an invariant alpha subunit and a substrate-specific beta subunit. The protein encoded by this gene is an ATP-specific SCS beta subunit that dimerizes with the SCS alpha subunit to form SCS-A, an essential component of the tricarboxylic acid cycle. SCS-A hydrolyzes ATP to convert succinate to succinyl-CoA. Defects in this gene are a cause of myopathic mitochondrial DNA depletion syndrome. A pseudogene of this gene has been found on chromosome 6. [provided by RefSeq, Jul 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCLA2	ENST00000643584.1	n.*214+16341G>T		intron_variant	Intron 13 of 13			ENSP00000494987.1
SUCLA2	ENST00000647008.1	n.1237+18030G>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60199 AN: 151900 Hom.: 12512 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.396 AC: 60228 AN: 152018 Hom.: 12516 Cov.: 32 AF XY: 0.386 AC XY: 28682 AN XY: 74294

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.383

Alfa AF: 0.379 Hom.: 6320

Bravo AF: 0.399

Asia WGS AF: 0.254 AC: 884 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	2.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7986369; hg19: chr13-48463123;