rs9268429

Variant names:

• chr6-32377275-A-G
• rs9268429
• ENST00000642577.1:n.168+11436A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642577.1(TSBP1-AS1):​n.168+11436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,478 control chromosomes in the GnomAD database, including 4,709 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 0.24 (4709 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 27 publications found

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-5689A>G		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+11436A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.168+11436A>G		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.125-9706A>G		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-12939A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37061 AN: 151360 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.245 AC: 37079 AN: 151478 Hom.: 4709 Cov.: 32 AF XY: 0.241 AC XY: 17812 AN XY: 74014

African (AFR) AF: 0.199 AC: 8217 AN: 41296

American (AMR) AF: 0.296 AC: 4504 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3460

East Asian (EAS) AF: 0.153 AC: 771 AN: 5036

South Asian (SAS) AF: 0.239 AC: 1120 AN: 4696

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18670 AN: 67890

Other (OTH) AF: 0.236 AC: 495 AN: 2098

Alfa AF: 0.277 Hom.: 6068

Bravo AF: 0.258

Asia WGS AF: 0.163 AC: 569 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9268429; hg19: chr6-32345052;