rs17527624

chr7-40645603-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUGCT	NM_001193313.2	c.1090-103831C>T		intron_variant		ENST00000335693.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUGCT	ENST00000335693.9	c.1090-103831C>T		intron_variant		1	NM_001193313.2	P1
SUGCT	ENST00000401647.7	c.946-103831C>T		intron_variant		1
SUGCT	ENST00000628514.3	c.1090-38453C>T		intron_variant		1

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

Gnomad4 AFR AF: 0.0440

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0975

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0678 Hom.: 186

Bravo AF: 0.0601

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.19
Dann	Benign	0.46

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: rs17527624; hg19: chr7-40685202;