7-40878471-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

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)

LOC105375242 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.669 AC: 27741 AN: 41484

American (AMR) AF: 0.549 AC: 8384 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4628 AN: 5146

South Asian (SAS) AF: 0.685 AC: 3300 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3749 AN: 10568

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29516 AN: 67990

Other (OTH) AF: 0.553 AC: 1164 AN: 2106

Alfa AF: 0.480 Hom.: 80958

Bravo AF: 0.553

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.044
DANN	Benign	0.58
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7801303; hg19: chr7-40918070;