7-40188456-C-A

Position:

• chr7-40188456-C-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001193313.2(SUGCT):​c.227-39C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.010 (4 hom., cov: 30)
  • Exomes 𝑓: 0.11 (15 hom.)
  • Failed GnomAD Quality Control
• Consequence: SUGCT NM_001193313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.14

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BP6: Variant 7-40188456-C-A is Benign according to our data. Variant chr7-40188456-C-A is described in ClinVar as [Benign]. Clinvar id is 1239377.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUGCT	NM_001193313.2	c.227-39C>A		intron_variant		ENST00000335693.9	NP_001180242.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUGCT	ENST00000335693.9	c.227-39C>A		intron_variant		1	NM_001193313.2	ENSP00000338475	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 1224 AN: 122202 Hom.: 4 Cov.: 30 FAILED QC

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00509

Gnomad ASJ AF: 0.00364

Gnomad EAS AF: 0.00778

Gnomad SAS AF: 0.00712

Gnomad FIN AF: 0.00902

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00635

Gnomad OTH AF: 0.0116

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.113 AC: 52540 AN: 464438 Hom.: 15 Cov.: 12 AF XY: 0.111 AC XY: 26856 AN XY: 242230

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.0996

Gnomad4 EAS exome AF: 0.0496

Gnomad4 SAS exome AF: 0.102

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.0819

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0101 AC: 1229 AN: 122234 Hom.: 4 Cov.: 30 AF XY: 0.0111 AC XY: 653 AN XY: 58912

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.00509

Gnomad4 ASJ AF: 0.00364

Gnomad4 EAS AF: 0.00758

Gnomad4 SAS AF: 0.00740

Gnomad4 FIN AF: 0.00902

Gnomad4 NFE AF: 0.00637

Gnomad4 OTH AF: 0.0127

Alfa AF: 0.0134 Hom.: 0

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	-1.1
CADD	Benign	0.13
DANN	Benign	0.28

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: rs774925854; hg19: chr7-40228055; COSMIC: COSV59336708;