chr3-67406609-G-A

Variant names:

• chr3-67406609-G-A
• rs62256378
• NM_003848.4:c.1063-5758C>T

Variant summary

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

The NM_003848.4(SUCLG2):​c.1063-5758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,248 control chromosomes in the GnomAD database, including 290 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 0.054 (290 hom., cov: 31)
• Consequence: SUCLG2 NM_003848.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG2	NM_003848.4	c.1063-5758C>T		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.1063-5758C>T		intron_variant	Intron 9 of 10	1	NM_003848.4	ENSP00000307432.5
SUCLG2	ENST00000493112.5	c.1063-5758C>T		intron_variant	Intron 9 of 10	1		ENSP00000419325.1
SUCLG2	ENST00000460567.5	c.334-5758C>T		intron_variant	Intron 3 of 4	1		ENSP00000417260.1

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8208 AN: 152130 Hom.: 290 Cov.: 31

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0539 AC: 8201 AN: 152248 Hom.: 290 Cov.: 31 AF XY: 0.0546 AC XY: 4060 AN XY: 74424

African (AFR) AF: 0.0134 AC: 557 AN: 41566

American (AMR) AF: 0.0567 AC: 866 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 272 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4828

European-Finnish (FIN) AF: 0.107 AC: 1129 AN: 10590

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5012 AN: 68008

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0634 Hom.: 783

Bravo AF: 0.0495

Asia WGS AF: 0.0100 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.63
PhyloP100		0.89
Mutation Taster		=99/1	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: rs62256378; hg19: chr3-67457033;