rs1490265

Positions:

• chr3-67401619-C-A
• chr3-67401619-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003848.4(SUCLG2):​c.1063-768G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 149,262 control chromosomes in the GnomAD database, including 41,064 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 0.74 (41064 hom., cov: 27)
• Consequence: SUCLG2 NM_003848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUCLG2	NM_003848.4	c.1063-768G>T		intron_variant		ENST00000307227.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUCLG2	ENST00000307227.10	c.1063-768G>T		intron_variant		1	NM_003848.4	P1
SUCLG2	ENST00000460567.5	c.335-768G>T		intron_variant		1
SUCLG2	ENST00000493112.5	c.1063-768G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 110209 AN: 149184 Hom.: 41040 Cov.: 27

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.739 AC: 110274 AN: 149262 Hom.: 41064 Cov.: 27 AF XY: 0.734 AC XY: 53251 AN XY: 72592

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.774

Alfa AF: 0.708 Hom.: 16814

Bravo AF: 0.760

Asia WGS AF: 0.636 AC: 2199 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	14
DANN	Benign	0.64

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: rs1490265; hg19: chr3-67452043;