6-32407503-C-G

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.1793C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 179,368 control chromosomes in the GnomAD database, including 8,841 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 0.31 ( 7360 hom., cov: 31)
Exomes 𝑓: 0.32 ( 1481 hom. )

Consequence

TSBP1-AS1
NR_136245.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.247
Variant links:
Genes affected

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=-0.61).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSBP1-AS1NR_136245.1 linkuse as main transcriptn.1793C>G non_coding_transcript_exon_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSBP1-AS1ENST00000642577.1 linkuse as main transcriptn.2323C>G non_coding_transcript_exon_variant 6/6
TSBP1-AS1ENST00000645134.1 linkuse as main transcriptn.2242C>G non_coding_transcript_exon_variant 5/5
TSBP1-AS1ENST00000645167.1 linkuse as main transcriptn.1510C>G non_coding_transcript_exon_variant 3/3

Frequencies

GnomAD3 genomes
AF:
0.308
AC:
46760
AN:
151854
Hom.:
7357
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.325
Gnomad AMI
AF:
0.241
Gnomad AMR
AF:
0.332
Gnomad ASJ
AF:
0.351
Gnomad EAS
AF:
0.359
Gnomad SAS
AF:
0.391
Gnomad FIN
AF:
0.221
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.295
Gnomad OTH
AF:
0.303
GnomAD4 exome
AF:
0.317
AC:
8674
AN:
27396
Hom.:
1481
Cov.:
0
AF XY:
0.320
AC XY:
4600
AN XY:
14362
show subpopulations
Gnomad4 AFR exome
AF:
0.324
Gnomad4 AMR exome
AF:
0.385
Gnomad4 ASJ exome
AF:
0.343
Gnomad4 EAS exome
AF:
0.344
Gnomad4 SAS exome
AF:
0.396
Gnomad4 FIN exome
AF:
0.199
Gnomad4 NFE exome
AF:
0.297
Gnomad4 OTH exome
AF:
0.306
GnomAD4 genome
AF:
0.308
AC:
46791
AN:
151972
Hom.:
7360
Cov.:
31
AF XY:
0.307
AC XY:
22778
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.325
Gnomad4 AMR
AF:
0.332
Gnomad4 ASJ
AF:
0.351
Gnomad4 EAS
AF:
0.360
Gnomad4 SAS
AF:
0.391
Gnomad4 FIN
AF:
0.221
Gnomad4 NFE
AF:
0.295
Gnomad4 OTH
AF:
0.302
Alfa
AF:
0.280
Hom.:
778
Bravo
AF:
0.323
Asia WGS
AF:
0.378
AC:
1320
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
2.5
DANN
Benign
0.87

Splicing

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: rs9268492; hg19: chr6-32375280; API