7-40925528-G-A

Variant names:

• chr7-40925528-G-A
• rs7789197
• ENST00000770551.1:n.107-19818G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000770551.1(ENSG00000300277):​n.107-19818G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,984 control chromosomes in the GnomAD database, including 7,096 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (7096 hom., cov: 32)
• Consequence: ENSG00000300277 ENST00000770551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 14 publications found

Genes affected

ENSG00000300277 (HGNC:):

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]

SUGCT Gene-Disease associations (from GenCC):

• glutaric acidemia type 3

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia, ClinGen, Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300277	ENST00000770551.1		n.107-19818G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40958 AN: 151866 Hom.: 7069 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.270 AC: 41032 AN: 151984 Hom.: 7096 Cov.: 32 AF XY: 0.271 AC XY: 20120 AN XY: 74296

African (AFR) AF: 0.490 AC: 20300 AN: 41450

American (AMR) AF: 0.157 AC: 2396 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 716 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1443 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1472 AN: 4808

European-Finnish (FIN) AF: 0.221 AC: 2326 AN: 10542

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11736 AN: 67970

Other (OTH) AF: 0.247 AC: 523 AN: 2114

Alfa AF: 0.201 Hom.: 16135

Bravo AF: 0.272

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.073
DANN	Benign	0.38
PhyloP100		-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7789197;

hg19: chr7-40965127;

COSMIC: COSV50192870;