7-40180876-A-G

Position:

• chr7-40180876-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.101-71A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 1,138,776 control chromosomes in the GnomAD database, including 1,771 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.039 (148 hom., cov: 33)
  • Exomes 𝑓: 0.052 (1623 hom.)
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.572

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=-0.9).
• BP6: Variant 7-40180876-A-G is Benign according to our data. Variant chr7-40180876-A-G is described in ClinVar as [Benign]. Clinvar id is 1222524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.07 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.101-71A>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.101-71A>G		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5883 AN: 152186 Hom.: 148 Cov.: 33

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0445

GnomAD4 exome AF: 0.0520 AC: 51251 AN: 986472 Hom.: 1623 AF XY: 0.0540 AC XY: 27616 AN XY: 511466

Gnomad4 AFR exome AF: 0.0122

Gnomad4 AMR exome AF: 0.0591

Gnomad4 ASJ exome AF: 0.0545

Gnomad4 EAS exome AF: 0.00209

Gnomad4 SAS exome AF: 0.0843

Gnomad4 FIN exome AF: 0.0294

Gnomad4 NFE exome AF: 0.0537

Gnomad4 OTH exome AF: 0.0499

GnomAD4 genome AF: 0.0386 AC: 5883 AN: 152304 Hom.: 148 Cov.: 33 AF XY: 0.0376 AC XY: 2803 AN XY: 74476

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0218 Hom.: 11

Bravo AF: 0.0393

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	-0.90
CADD	Benign	1.0
DANN	Benign	0.56

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: rs116844030; hg19: chr7-40220475;