rs4959093

Positions:

• chr6-32345320-T-C

Variant summary

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

The NM_001286474.2(TSBP1):​c.281-2062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,920 control chromosomes in the GnomAD database, including 9,642 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 0.34 (9642 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

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

TSBP1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.281-2062A>G		intron_variant		ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.281-2062A>G		intron_variant		1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51027 AN: 151802 Hom.: 9629 Cov.: 30

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.336 AC: 51055 AN: 151920 Hom.: 9642 Cov.: 30 AF XY: 0.336 AC XY: 24974 AN XY: 74244

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.352

Alfa AF: 0.391 Hom.: 4278

Bravo AF: 0.342

Asia WGS AF: 0.343 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.68

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: rs4959093; hg19: chr6-32313097;