Variant 7-40188479-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000335693.9(SUGCT):c.227-16A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,476,716 control chromosomes in the GnomAD database, including 18,295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1831 hom., cov: 31)

Exomes 𝑓: 0.14 ( 16464 hom. )

Consequence

SUGCT
ENST00000335693.9 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.77

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 7-40188479-A-T is Benign according to our data. Variant chr7-40188479-A-T is described in ClinVar as [Benign]. Clinvar id is 559088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2 linkuse as main transcript	c.227-16A>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9 linkuse as main transcript	c.227-16A>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18165

AN:

150566

Hom.:

1828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.0964

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.132

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.112

GnomAD3 exomes

AF:

0.172

AC:

37247

AN:

216012

Hom.:

4499

AF XY:

0.174

AC XY:

20414

AN XY:

117346

show subpopulations

Gnomad AFR exome

AF:

0.0220

Gnomad AMR exome

AF:

0.249

Gnomad ASJ exome

AF:

0.0949

Gnomad EAS exome

AF:

0.421

Gnomad SAS exome

AF:

0.287

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.156

GnomAD4 exome

AF:

0.139

AC:

184012

AN:

1326054

Hom.:

16464

Cov.:

AF XY:

0.143

AC XY:

94911

AN XY:

664108

show subpopulations

Gnomad4 AFR exome

AF:

0.0200

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.0943

Gnomad4 EAS exome

AF:

0.401

Gnomad4 SAS exome

AF:

0.293

Gnomad4 FIN exome

AF:

0.210

Gnomad4 NFE exome

AF:

0.114

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.121

AC:

18168

AN:

150662

Hom.:

1831

Cov.:

AF XY:

0.133

AC XY:

9732

AN XY:

73428

show subpopulations

Gnomad4 AFR

AF:

0.0244

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.0964

Gnomad4 EAS

AF:

0.439

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.116

Alfa

AF:

0.0724

Hom.:

155

Bravo

AF:

0.113

Asia WGS

AF:

0.361

AC:

1254

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 15, 2015	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Benign

0.89

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over