rs2050189

chr6-32371870-T-Cchr6-32371870-T-G

Variant summary

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

The NM_001286474.2(TSBP1):c.-164A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 724,760 control chromosomes in the GnomAD database, including 21,496 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 0.19 (3371 hom., cov: 32)
  • Exomes 𝑓: 0.24 (18125 hom.)
• Consequence: TSBP1 NM_001286474.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.-164A>G		5_prime_UTR_variant	1/26	ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.302+6031T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.-164A>G		5_prime_UTR_variant	1/26	1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.88-18344T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28819 AN: 152092 Hom.: 3348 Cov.: 32

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.239 AC: 136573 AN: 572550 Hom.: 18125 Cov.: 7 AF XY: 0.244 AC XY: 74934 AN XY: 306674

Gnomad4 AFR exome AF: 0.0737

Gnomad4 AMR exome AF: 0.345

Gnomad4 ASJ exome AF: 0.159

Gnomad4 EAS exome AF: 0.341

Gnomad4 SAS exome AF: 0.350

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.216

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.190 AC: 28867 AN: 152210 Hom.: 3371 Cov.: 32 AF XY: 0.193 AC XY: 14374 AN XY: 74434

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.211

Alfa AF: 0.223 Hom.: 7077

Bravo AF: 0.188

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.5
Dann	Benign	0.78

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: rs2050189; hg19: chr6-32339647; COSMIC: COSV66658378;