7-40181746-C-CA

Position:

• chr7-40181746-C-CA

Variant summary

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

The NM_001193313.2(SUGCT):​c.153-195dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.35 (5627 hom., cov: 20)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.01

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 7-40181746-C-CA is Benign according to our data. Variant chr7-40181746-C-CA is described in ClinVar as [Benign]. Clinvar id is 1281060.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.153-195dup		intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.153-195dup		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 36708 AN: 103596 Hom.: 5633 Cov.: 20

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.354 AC: 36687 AN: 103622 Hom.: 5627 Cov.: 20 AF XY: 0.362 AC XY: 18105 AN XY: 50066

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.379

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: rs35533534; hg19: chr7-40221345;