7-40878471-A-G

Variant names:

• chr7-40878471-A-G
• rs7801303
• XM_047420840.1:c.1310-3210A>G

Variant summary

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

The XM_047420840.1(SUGCT):​c.1310-3210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,064 control chromosomes in the GnomAD database, including 22,853 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 0.53 (22853 hom., cov: 32)
• Consequence: SUGCT XM_047420840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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]

LOC105375242 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUGCT	XM_047420840.1	c.1310-3210A>G		intron_variant	Intron 15 of 15		XP_047276796.1
SUGCT	XM_047420843.1	c.1154-3210A>G		intron_variant	Intron 13 of 13		XP_047276799.1
LOC105375242	XR_001745181.2	n.537-12323T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80856 AN: 151948 Hom.: 22813 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.532 AC: 80951 AN: 152064 Hom.: 22853 Cov.: 32 AF XY: 0.534 AC XY: 39688 AN XY: 74320

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.553

Alfa AF: 0.471 Hom.: 35930

Bravo AF: 0.553

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.044
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7801303; hg19: chr7-40918070;