6-32373621-A-G

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.302+7782A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,188 control chromosomes in the GnomAD database, including 1,560 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 0.13 ( 1560 hom., cov: 32)

Consequence

TSBP1-AS1
NR_136245.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.332
Variant links:
Genes affected
TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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.302+7782A>G intron_variant, non_coding_transcript_variant
TSBP1-AS1NR_136244.1 linkuse as main transcriptn.500+7782A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSBP1-AS1ENST00000645134.1 linkuse as main transcriptn.88-16593A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.134
AC:
20452
AN:
152070
Hom.:
1559
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0950
Gnomad AMI
AF:
0.394
Gnomad AMR
AF:
0.0934
Gnomad ASJ
AF:
0.0573
Gnomad EAS
AF:
0.127
Gnomad SAS
AF:
0.148
Gnomad FIN
AF:
0.247
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.151
Gnomad OTH
AF:
0.123
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.134
AC:
20464
AN:
152188
Hom.:
1560
Cov.:
32
AF XY:
0.138
AC XY:
10299
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0950
Gnomad4 AMR
AF:
0.0932
Gnomad4 ASJ
AF:
0.0573
Gnomad4 EAS
AF:
0.127
Gnomad4 SAS
AF:
0.149
Gnomad4 FIN
AF:
0.247
Gnomad4 NFE
AF:
0.151
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.138
Hom.:
1826
Bravo
AF:
0.119
Asia WGS
AF:
0.134
AC:
470
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
6.5
DANN
Benign
0.56

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: rs9391858; hg19: chr6-32341398; API