rs9268301

Variant names:

• chr6-32351860-G-A
• rs9268301
• NM_001286474.2:c.260-2100C>T

Variant summary

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

The NM_001286474.2(TSBP1):​c.260-2100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,700 control chromosomes in the GnomAD database, including 6,985 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 0.29 (6985 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847
• Publications: 16 publications found

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.260-2100C>T		intron_variant	Intron 8 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.260-2100C>T		intron_variant	Intron 8 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43631 AN: 151580 Hom.: 6985 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.288 AC: 43652 AN: 151700 Hom.: 6985 Cov.: 32 AF XY: 0.286 AC XY: 21170 AN XY: 74092

African (AFR) AF: 0.149 AC: 6163 AN: 41396

American (AMR) AF: 0.375 AC: 5728 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1624 AN: 3458

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4808

European-Finnish (FIN) AF: 0.237 AC: 2487 AN: 10480

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23558 AN: 67820

Other (OTH) AF: 0.292 AC: 614 AN: 2106

Alfa AF: 0.324 Hom.: 12745

Bravo AF: 0.295

Asia WGS AF: 0.269 AC: 940 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	0.69
DANN	Benign	0.24
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9268301; hg19: chr6-32319637;