ENST00000770551.1:n.106+15287A>G

Variant names:

• chr7-40914882-A-G
• rs29880
• ENST00000770551.1:n.106+15287A>G

Variant summary

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

The ENST00000770551.1(ENSG00000300277):​n.106+15287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,160 control chromosomes in the GnomAD database, including 2,107 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 0.15 (2107 hom., cov: 32)
• Consequence: ENSG00000300277 ENST00000770551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 10 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: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUGCT	XR_007060157.1	n.1343+33028A>G		intron_variant	Intron 14 of 15
SUGCT	XR_007060158.1	n.1199+33028A>G		intron_variant	Intron 13 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300277	ENST00000770551.1	n.106+15287A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23313 AN: 152042 Hom.: 2100 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.153 AC: 23337 AN: 152160 Hom.: 2107 Cov.: 32 AF XY: 0.152 AC XY: 11272 AN XY: 74392

African (AFR) AF: 0.255 AC: 10578 AN: 41474

American (AMR) AF: 0.104 AC: 1595 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.114 AC: 592 AN: 5172

South Asian (SAS) AF: 0.145 AC: 701 AN: 4818

European-Finnish (FIN) AF: 0.128 AC: 1361 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7498 AN: 68004

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.125 Hom.: 6224

Bravo AF: 0.154

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.70
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs29880; hg19: chr7-40954481;