7-40180813-T-C

Position:

• chr7-40180813-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000335693.9(SUGCT):​c.101-134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 665,144 control chromosomes in the GnomAD database, including 91,785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.58 (27210 hom., cov: 32)
  • Exomes 𝑓: 0.49 (64575 hom.)
• Consequence: SUGCT ENST00000335693.9 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.617

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 7-40180813-T-C is Benign according to our data. Variant chr7-40180813-T-C is described in ClinVar as [Benign]. Clinvar id is 1220785.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.101-134T>C		intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.101-134T>C		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87510 AN: 151928 Hom.: 27158 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.569

GnomAD4 exome AF: 0.494 AC: 253702 AN: 513098 Hom.: 64575 AF XY: 0.499 AC XY: 137490 AN XY: 275318

Gnomad4 AFR exome AF: 0.824

Gnomad4 AMR exome AF: 0.496

Gnomad4 ASJ exome AF: 0.570

Gnomad4 EAS exome AF: 0.403

Gnomad4 SAS exome AF: 0.597

Gnomad4 FIN exome AF: 0.468

Gnomad4 NFE exome AF: 0.471

Gnomad4 OTH exome AF: 0.515

GnomAD4 genome AF: 0.576 AC: 87623 AN: 152046 Hom.: 27210 Cov.: 32 AF XY: 0.576 AC XY: 42833 AN XY: 74302

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.574

Alfa AF: 0.514 Hom.: 6507

Bravo AF: 0.590

Asia WGS AF: 0.551 AC: 1917 AN: 3478

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

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.68

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: rs7778061; hg19: chr7-40220412; COSMIC: COSV59318801;