3-67360748-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000493112.5(SUCLG2):c.1203del(p.Gly402GlufsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,507,606 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0063 (10 hom., cov: 32)
  • Exomes 𝑓: 0.00080 (11 hom.)
• Consequence: SUCLG2 ENST00000493112.5 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0550

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.

• BP6: Variant 3-67360748-CT-C is Benign according to our data. Variant chr3-67360748-CT-C is described in ClinVar as [Benign]. Clinvar id is 791936.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00634 (963/151962) while in subpopulation AFR AF= 0.0216 (896/41440). AF 95% confidence interval is 0.0204. There are 10 homozygotes in gnomad4. There are 440 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUCLG2	NM_001177599.2	c.1203del	p.Gly402GlufsTer6	frameshift_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUCLG2	ENST00000493112.5	c.1203del	p.Gly402GlufsTer6	frameshift_variant	11/11	1

Frequencies

GnomAD3 genomes AF: 0.00635 AC: 964 AN: 151844 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00322

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00528

GnomAD3 exomes AF: 0.00150 AC: 174 AN: 115926 Hom.: 0 AF XY: 0.00118 AC XY: 75 AN XY: 63334

Gnomad AFR exome AF: 0.0200

Gnomad AMR exome AF: 0.00156

Gnomad ASJ exome AF: 0.000961

Gnomad EAS exome AF: 0.000110

Gnomad SAS exome AF: 0.0000540

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000232

Gnomad OTH exome AF: 0.00140

GnomAD4 exome AF: 0.000803 AC: 1088 AN: 1355644 Hom.: 11 Cov.: 29 AF XY: 0.000765 AC XY: 511 AN XY: 667986

Gnomad4 AFR exome AF: 0.0226

Gnomad4 AMR exome AF: 0.00150

Gnomad4 ASJ exome AF: 0.00103

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000284

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000195

Gnomad4 OTH exome AF: 0.00164

GnomAD4 genome AF: 0.00634 AC: 963 AN: 151962 Hom.: 10 Cov.: 32 AF XY: 0.00592 AC XY: 440 AN XY: 74280

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.00321

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00522

Alfa AF: 0.000205 Hom.: 0

Bravo AF: 0.00770

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201326682; hg19: chr3-67411172;