rs4379368

Positions:

• chr7-40426601-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.817-22686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,026 control chromosomes in the GnomAD database, including 1,590 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 0.13 (1590 hom., cov: 32)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUGCT	NM_001193313.2	c.817-22686C>T		intron_variant		ENST00000335693.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUGCT	ENST00000335693.9	c.817-22686C>T		intron_variant		1	NM_001193313.2	P1
SUGCT	ENST00000401647.7	c.673-22686C>T		intron_variant		1
SUGCT	ENST00000416370.2	c.817-22686C>T		intron_variant		1
SUGCT	ENST00000628514.3	c.817-22686C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18997 AN: 151908 Hom.: 1587 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.125 AC: 19012 AN: 152026 Hom.: 1590 Cov.: 32 AF XY: 0.128 AC XY: 9521 AN XY: 74284

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.110

Alfa AF: 0.113 Hom.: 443

Bravo AF: 0.125

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.76

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: rs4379368; hg19: chr7-40466200;