7-40180908-C-G

Position:

• chr7-40180908-C-G

Variant summary

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

The NM_001193313.2(SUGCT):​c.101-39C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,434,000 control chromosomes in the GnomAD database, including 166,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (20197 hom., cov: 32)
  • Exomes 𝑓: 0.47 (146537 hom.)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.54

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=-0.92).
• BP6: Variant 7-40180908-C-G is Benign according to our data. Variant chr7-40180908-C-G is described in ClinVar as [Benign]. Clinvar id is 1273460.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.101-39C>G		intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.101-39C>G		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77483 AN: 151842 Hom.: 20179 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.526

GnomAD3 exomes AF: 0.496 AC: 120824 AN: 243488 Hom.: 30669 AF XY: 0.500 AC XY: 66110 AN XY: 132126

Gnomad AFR exome AF: 0.599

Gnomad AMR exome AF: 0.485

Gnomad ASJ exome AF: 0.571

Gnomad EAS exome AF: 0.438

Gnomad SAS exome AF: 0.592

Gnomad FIN exome AF: 0.462

Gnomad NFE exome AF: 0.469

Gnomad OTH exome AF: 0.507

GnomAD4 exome AF: 0.474 AC: 607884 AN: 1282040 Hom.: 146537 Cov.: 18 AF XY: 0.479 AC XY: 310006 AN XY: 646730

Gnomad4 AFR exome AF: 0.596

Gnomad4 AMR exome AF: 0.481

Gnomad4 ASJ exome AF: 0.570

Gnomad4 EAS exome AF: 0.408

Gnomad4 SAS exome AF: 0.595

Gnomad4 FIN exome AF: 0.468

Gnomad4 NFE exome AF: 0.458

Gnomad4 OTH exome AF: 0.497

GnomAD4 genome AF: 0.510 AC: 77544 AN: 151960 Hom.: 20197 Cov.: 32 AF XY: 0.512 AC XY: 38019 AN XY: 74244

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.531

Alfa AF: 0.447 Hom.: 2341

Bravo AF: 0.515

Asia WGS AF: 0.531 AC: 1847 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	-0.92
CADD	Benign	0.23
DANN	Benign	0.57

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: rs2036041; hg19: chr7-40220507; COSMIC: COSV59313173;