rs9268429

Positions:

• chr6-32377275-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136245.1(TSBP1-AS1):​n.302+11436A>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 0.245 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 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+11436A>G		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-5689A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-12939A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.236

Alfa AF: 0.263 Hom.: 1878

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268429; hg19: chr6-32345052;