rs2076537

Positions:

• chr6-32349858-G-A
• chr6-32349858-G-C
• chr6-32349858-G-T

Variant summary

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

The NM_001286474.2(TSBP1):​c.260-98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 1,347,764 control chromosomes in the GnomAD database, including 103,886 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 0.42 (14395 hom., cov: 32)
  • Exomes 𝑓: 0.38 (89491 hom.)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.260-98C>T		intron_variant		ENST00000533191.6	NP_001273403.1
TSBP1-AS1	NR_136245.1	n.243-15922G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.260-98C>T		intron_variant		1	NM_001286474.2	ENSP00000431199	A2
TSBP1-AS1	ENST00000645134.1	n.88-40356G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64007 AN: 151864 Hom.: 14371 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.382

GnomAD3 exomes AF: 0.375 AC: 92017 AN: 245454 Hom.: 18403 AF XY: 0.375 AC XY: 50136 AN XY: 133816

Gnomad AFR exome AF: 0.556

Gnomad AMR exome AF: 0.262

Gnomad ASJ exome AF: 0.233

Gnomad EAS exome AF: 0.393

Gnomad SAS exome AF: 0.394

Gnomad FIN exome AF: 0.526

Gnomad NFE exome AF: 0.361

Gnomad OTH exome AF: 0.355

GnomAD4 exome AF: 0.381 AC: 455408 AN: 1195782 Hom.: 89491 Cov.: 16 AF XY: 0.380 AC XY: 230948 AN XY: 607790

Gnomad4 AFR exome AF: 0.557

Gnomad4 AMR exome AF: 0.265

Gnomad4 ASJ exome AF: 0.235

Gnomad4 EAS exome AF: 0.492

Gnomad4 SAS exome AF: 0.393

Gnomad4 FIN exome AF: 0.524

Gnomad4 NFE exome AF: 0.372

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.422 AC: 64073 AN: 151982 Hom.: 14395 Cov.: 32 AF XY: 0.426 AC XY: 31670 AN XY: 74296

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.383

Alfa AF: 0.345 Hom.: 5010

Bravo AF: 0.405

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076537; hg19: chr6-32317635; COSMIC: COSV66657630; COSMIC: COSV66657630;