rs17806888

Positions:

• chr3-67365898-T-C
• chr3-67365898-T-G

Variant summary

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

The ENST00000493112.5(SUCLG2):​c.1184-5130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 152,280 control chromosomes in the GnomAD database, including 743 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 0.091 (743 hom., cov: 32)
• Consequence: SUCLG2 ENST00000493112.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG2	NM_001177599.2	c.1184-5130A>G		intron_variant			NP_001171070.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG2	ENST00000493112.5	c.1184-5130A>G		intron_variant		1		ENSP00000419325

Frequencies

GnomAD3 genomes AF: 0.0914 AC: 13913 AN: 152162 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.0913 AC: 13898 AN: 152280 Hom.: 743 Cov.: 32 AF XY: 0.0873 AC XY: 6499 AN XY: 74458

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0418

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.127

Alfa AF: 0.121 Hom.: 2359

Bravo AF: 0.0945

Asia WGS AF: 0.0450 AC: 158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17806888; hg19: chr3-67416322;