3-67648947-A-G

Position:

• chr3-67648947-A-G

Variant summary

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

The NM_003848.4(SUCLG2):​c.84+5556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,090 control chromosomes in the GnomAD database, including 9,729 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 0.35 (9729 hom., cov: 32)
• Consequence: SUCLG2 NM_003848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUCLG2	NM_003848.4	c.84+5556T>C		intron_variant		ENST00000307227.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUCLG2	ENST00000307227.10	c.84+5556T>C		intron_variant		1	NM_003848.4	P1
SUCLG2	ENST00000493112.5	c.84+5556T>C		intron_variant		1
SUCLG2	ENST00000492795.1	c.84+5556T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53610 AN: 151972 Hom.: 9718 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.353 AC: 53644 AN: 152090 Hom.: 9729 Cov.: 32 AF XY: 0.348 AC XY: 25912 AN XY: 74368

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.351

Alfa AF: 0.354 Hom.: 16319

Bravo AF: 0.344

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.52

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: rs935734; hg19: chr3-67699371;