rs9839894

Variant names:

• chr3-67465715-T-C
• rs9839894
• NM_003848.4:c.1062+30083A>G

Variant summary

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

The NM_003848.4(SUCLG2):​c.1062+30083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,190 control chromosomes in the GnomAD database, including 991 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 0.10 (991 hom., cov: 32)
• Consequence: SUCLG2 NM_003848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG2	NM_003848.4	c.1062+30083A>G		intron_variant	Intron 9 of 10	ENST00000307227.10	NP_003839.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCLG2	ENST00000307227.10	c.1062+30083A>G		intron_variant	Intron 9 of 10	1	NM_003848.4	ENSP00000307432.5
SUCLG2	ENST00000493112.5	c.1062+30083A>G		intron_variant	Intron 9 of 10	1		ENSP00000419325.1
SUCLG2	ENST00000460567.5	c.333+52532A>G		intron_variant	Intron 3 of 4	1		ENSP00000417260.1
SUCLG2	ENST00000492795.1	c.1062+30083A>G		intron_variant	Intron 9 of 9	2		ENSP00000417589.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15288 AN: 152072 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.101 AC: 15303 AN: 152190 Hom.: 991 Cov.: 32 AF XY: 0.101 AC XY: 7490 AN XY: 74418

African (AFR) AF: 0.163 AC: 6758 AN: 41516

American (AMR) AF: 0.0873 AC: 1335 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.248 AC: 1273 AN: 5140

South Asian (SAS) AF: 0.117 AC: 565 AN: 4822

European-Finnish (FIN) AF: 0.0495 AC: 526 AN: 10616

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4320 AN: 68026

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0810 Hom.: 77

Bravo AF: 0.106

Asia WGS AF: 0.166 AC: 576 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.72
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9839894; hg19: chr3-67516139;