rs2363709

Variant names:

• chr3-67366681-G-A
• rs2363709
• ENST00000493112.5:c.1184-5913C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-67366681-G-A
• chr3-67366681-G-C
• chr3-67366681-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001177599.2(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 NM_001177599.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001177599.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUCLG2	NM_001177599.2		c.1184-5913C>T		intron	N/A	NP_001171070.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUCLG2	ENST00000493112.5	TSL:1	c.1184-5913C>T		intron	N/A	ENSP00000419325.1

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

African (AFR) AF: 0.879 AC: 36476 AN: 41500

American (AMR) AF: 0.828 AC: 12661 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3401 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5097 AN: 5170

South Asian (SAS) AF: 0.885 AC: 4266 AN: 4818

European-Finnish (FIN) AF: 0.940 AC: 9963 AN: 10598

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63682 AN: 68034

Other (OTH) AF: 0.925 AC: 1956 AN: 2114

Alfa AF: 0.920 Hom.: 8341

Bravo AF: 0.901

Asia WGS AF: 0.915 AC: 3179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.015
DANN	Benign	0.45
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2363709; hg19: chr3-67417105;