rs17688601

Variant names:

• chr7-40827064-C-A
• rs17688601
• NM_001193313.2:c.1154-33252C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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]

SUGCT Gene-Disease associations (from GenCC):

• glutaric acidemia type 3

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)

LOC112267984 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001193313.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGCT	NM_001193313.2	MANE Select	c.1154-33252C>A		intron	N/A	NP_001180242.2	Q9HAC7-1
	SUGCT	NM_001193311.2		c.1232-33252C>A		intron	N/A	NP_001180240.2	Q9HAC7-3
	SUGCT	NM_024728.3		c.1121-33252C>A		intron	N/A	NP_079004.2	Q9HAC7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGCT	ENST00000335693.9	TSL:1 MANE Select	c.1154-33252C>A		intron	N/A	ENSP00000338475.5	Q9HAC7-1
	SUGCT	ENST00000628514.3	TSL:1	c.1232-33252C>A		intron	N/A	ENSP00000486291.2	Q9HAC7-3
	SUGCT	ENST00000401647.7	TSL:1	c.1010-33252C>A		intron	N/A	ENSP00000385222.3	Q9HAC7-4

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

African (AFR) AF: 0.0647 AC: 2685 AN: 41502

American (AMR) AF: 0.218 AC: 3336 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3468

East Asian (EAS) AF: 0.0445 AC: 230 AN: 5174

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4816

European-Finnish (FIN) AF: 0.274 AC: 2887 AN: 10554

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17952 AN: 67984

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.244 Hom.: 19163

Bravo AF: 0.187

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.39
PhyloP100		-0.82
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: rs17688601; hg19: chr7-40866663;