3-67648947-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003848.4(SUCLG2):​c.84+5556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,090 control chromosomes in the GnomAD database, including 9,729 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 0.35 ( 9729 hom., cov: 32)

Consequence

SUCLG2
NM_003848.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.332
Variant links:
Genes affected
SUCLG2 (HGNC:11450): (succinate-CoA ligase GDP-forming subunit beta) This gene encodes a GTP-specific beta subunit of succinyl-CoA synthetase. Succinyl-CoA synthetase catalyzes the reversible reaction involving the formation of succinyl-CoA and succinate. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 5 and 12. [provided by RefSeq, Apr 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SUCLG2NM_003848.4 linkuse as main transcriptc.84+5556T>C intron_variant ENST00000307227.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SUCLG2ENST00000307227.10 linkuse as main transcriptc.84+5556T>C intron_variant 1 NM_003848.4 P1Q96I99-1
SUCLG2ENST00000493112.5 linkuse as main transcriptc.84+5556T>C intron_variant 1 Q96I99-2
SUCLG2ENST00000492795.1 linkuse as main transcriptc.84+5556T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.353
AC:
53610
AN:
151972
Hom.:
9718
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.375
Gnomad AMI
AF:
0.351
Gnomad AMR
AF:
0.282
Gnomad ASJ
AF:
0.380
Gnomad EAS
AF:
0.299
Gnomad SAS
AF:
0.198
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.362
Gnomad OTH
AF:
0.346
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.353
AC:
53644
AN:
152090
Hom.:
9729
Cov.:
32
AF XY:
0.348
AC XY:
25912
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.375
Gnomad4 AMR
AF:
0.281
Gnomad4 ASJ
AF:
0.380
Gnomad4 EAS
AF:
0.299
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.396
Gnomad4 NFE
AF:
0.362
Gnomad4 OTH
AF:
0.351
Alfa
AF:
0.354
Hom.:
16319
Bravo
AF:
0.344
Asia WGS
AF:
0.296
AC:
1028
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
2.9
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs935734; hg19: chr3-67699371; API