rs2363709

chr3-67366681-G-Achr3-67366681-G-Cchr3-67366681-G-T

Variant summary

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

The ENST00000493112.5(SUCLG2):c.1184-5913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,206 control chromosomes in the GnomAD database, including 63,323 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 0.91 (63323 hom., cov: 32)
• Consequence: SUCLG2 ENST00000493112.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

SUCLG2 (HGNC:11450): (succinate-CoA ligase GDP-forming subunit beta) This gene encodes a GTP-specific beta subunit of succinyl-CoA synthetase. Succinyl-CoA synthetase catalyzes the reversible reaction involving the formation of succinyl-CoA and succinate. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 5 and 12. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUCLG2	NM_001177599.2	c.1184-5913C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUCLG2	ENST00000493112.5	c.1184-5913C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138534 AN: 152088 Hom.: 63288 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.911 AC: 138625 AN: 152206 Hom.: 63323 Cov.: 32 AF XY: 0.910 AC XY: 67723 AN XY: 74396

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.940

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.925

Alfa AF: 0.922 Hom.: 8035

Bravo AF: 0.901

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.015
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2363709; hg19: chr3-67417105;