7-40188432-T-TC

Position:

• chr7-40188432-T-TC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000335693.9(SUGCT):​c.227-61dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 700,474 control chromosomes in the GnomAD database, including 4,146 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (2352 hom., cov: 0)
  • Exomes 𝑓: 0.11 (1794 hom.)
• Consequence: SUGCT ENST00000335693.9 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.736

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 -10 ACMG points.

• BP6: Variant 7-40188432-T-TC is Benign according to our data. Variant chr7-40188432-T-TC is described in ClinVar as [Benign]. Clinvar id is 1270855.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.227-61dup		intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.227-61dup		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 23867 AN: 86628 Hom.: 2353 Cov.: 0

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.113 AC: 69525 AN: 613848 Hom.: 1794 AF XY: 0.113 AC XY: 35876 AN XY: 317604

Gnomad4 AFR exome AF: 0.0356

Gnomad4 AMR exome AF: 0.113

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.0700

Gnomad4 SAS exome AF: 0.0996

Gnomad4 FIN exome AF: 0.0804

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.113

GnomAD4 genome AF: 0.275 AC: 23862 AN: 86626 Hom.: 2352 Cov.: 0 AF XY: 0.277 AC XY: 11007 AN XY: 39806

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.288

Asia WGS AF: 0.0700 AC: 236 AN: 3348

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs60252112; hg19: chr7-40228031;