rs29880

Variant names:

• chr7-40914882-A-G
• rs29880
• XR_007060157.1:n.1343+33028A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060157.1(SUGCT):​n.1343+33028A>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: SUGCT XR_007060157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724

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 -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

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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.147

Alfa AF: 0.120 Hom.: 2677

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs29880; hg19: chr7-40954481;