rs13196329

chr6-32357594-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001286474.2(TSBP1):c.218-1925T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 152,292 control chromosomes in the GnomAD database, including 79 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 0.026 (79 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

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).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0264 (4022/152292) while in subpopulation AFR AF= 0.0483 (2007/41562). AF 95% confidence interval is 0.0465. There are 79 homozygotes in gnomad4. There are 1988 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 78 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.218-1925T>G		intron_variant		ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.243-8186A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.218-1925T>G		intron_variant		1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.88-32620A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4023 AN: 152174 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.00857

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0264 AC: 4022 AN: 152292 Hom.: 79 Cov.: 32 AF XY: 0.0267 AC XY: 1988 AN XY: 74468

Gnomad4 AFR AF: 0.0483

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.00857

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0220 Hom.: 29

Bravo AF: 0.0298

Asia WGS AF: 0.0430 AC: 154 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	0.35
Dann	Benign	0.71

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: rs13196329; hg19: chr6-32325371;