7-40188313-A-G

Position:

• chr7-40188313-A-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.227-182A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 152,000 control chromosomes in the GnomAD database, including 144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.039 (144 hom., cov: 30)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.288

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 7-40188313-A-G is Benign according to our data. Variant chr7-40188313-A-G is described in ClinVar as [Benign]. Clinvar id is 1283528.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.227-182A>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.227-182A>G		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5880 AN: 151884 Hom.: 144 Cov.: 30

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0429

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

GnomAD4 genome AF: 0.0387 AC: 5880 AN: 152000 Hom.: 144 Cov.: 30 AF XY: 0.0377 AC XY: 2798 AN XY: 74298

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.00407

Gnomad4 SAS AF: 0.0759

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0419

Alfa AF: 0.0454 Hom.: 26

Bravo AF: 0.0394

Asia WGS AF: 0.0390 AC: 136 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 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.51

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: rs138579332; hg19: chr7-40227912;