rs9268499

Variant names:

• chr6-32407918-G-A
• rs9268499
• ENST00000642577.1:n.*155G>A

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.*188G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,964 control chromosomes in the GnomAD database, including 6,957 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 0.30 (6957 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 26 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_136245.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	NR_136245.1		n.*188G>A		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.*155G>A		downstream_gene	N/A
	TSBP1-AS1	ENST00000645134.1		n.*155G>A		downstream_gene	N/A
	TSBP1-AS1	ENST00000645167.1		n.*244G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45115 AN: 151846 Hom.: 6956 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.297 AC: 45140 AN: 151964 Hom.: 6957 Cov.: 32 AF XY: 0.298 AC XY: 22117 AN XY: 74308

African (AFR) AF: 0.277 AC: 11468 AN: 41406

American (AMR) AF: 0.324 AC: 4951 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2344 AN: 5172

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4830

European-Finnish (FIN) AF: 0.213 AC: 2244 AN: 10548

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19777 AN: 67940

Other (OTH) AF: 0.287 AC: 604 AN: 2104

Alfa AF: 0.304 Hom.: 13586

Bravo AF: 0.308

Asia WGS AF: 0.415 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.65
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9268499; hg19: chr6-32375695;