rs17527624

Variant names:

• chr7-40645603-C-T
• rs17527624
• NM_001193313.2:c.1090-103831C>T

Variant summary

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

The NM_001193313.2(SUGCT):​c.1090-103831C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0595 in 152,280 control chromosomes in the GnomAD database, including 295 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 0.060 (295 hom., cov: 32)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 0 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: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGCT	NM_001193313.2	MANE Select	c.1090-103831C>T		intron	N/A	NP_001180242.2
	SUGCT	NM_001193311.2		c.1090-38453C>T		intron	N/A	NP_001180240.2
	SUGCT	NM_024728.3		c.979-38453C>T		intron	N/A	NP_079004.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGCT	ENST00000335693.9	TSL:1 MANE Select	c.1090-103831C>T		intron	N/A	ENSP00000338475.5
	SUGCT	ENST00000628514.3	TSL:1	c.1090-38453C>T		intron	N/A	ENSP00000486291.2
	SUGCT	ENST00000401647.7	TSL:1	c.946-103831C>T		intron	N/A	ENSP00000385222.3

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9064 AN: 152162 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0595 AC: 9063 AN: 152280 Hom.: 295 Cov.: 32 AF XY: 0.0582 AC XY: 4335 AN XY: 74462

African (AFR) AF: 0.0440 AC: 1829 AN: 41546

American (AMR) AF: 0.0613 AC: 937 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0391 AC: 189 AN: 4830

European-Finnish (FIN) AF: 0.0418 AC: 444 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5072 AN: 68024

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0681 Hom.: 218

Bravo AF: 0.0601

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.46
PhyloP100		-1.5
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: rs17527624; hg19: chr7-40685202;