rs17688601

Positions:

• chr7-40827064-C-A

Variant summary

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

The NM_001193313.2(SUGCT):​c.1154-33252C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,090 control chromosomes in the GnomAD database, including 3,762 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 0.20 (3762 hom., cov: 32)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

Genes affected

SUGCT (HGNC:16001): (succinyl-CoA:glutarate-CoA transferase) This gene encodes a protein that is similar to members of the CaiB/baiF CoA-transferase protein family. Mutations in this gene are associated with glutaric aciduria type III. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

LOC112267984 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.1154-33252C>A		intron_variant		ENST00000335693.9	NP_001180242.2
LOC112267984	XR_007060292.1	n.2048G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.1154-33252C>A		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30507 AN: 151972 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.201 AC: 30514 AN: 152090 Hom.: 3762 Cov.: 32 AF XY: 0.204 AC XY: 15159 AN XY: 74348

Gnomad4 AFR AF: 0.0647

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0445

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.237

Alfa AF: 0.257 Hom.: 9482

Bravo AF: 0.187

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.39

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: rs17688601; hg19: chr7-40866663;