rs3132959

Variant names:

• chr6-32331165-G-A
• rs3132959
• NM_001286474.2:c.446-556C>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.446-556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,048 control chromosomes in the GnomAD database, including 45,118 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 0.77 (45118 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 36 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286474.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	NM_001286474.2	MANE Select	c.446-556C>T		intron	N/A	NP_001273403.1	A0A1U9X7D1
	TSBP1	NM_006781.5		c.494-556C>T		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.425-556C>T		intron	N/A	NP_001273404.1	E9PLW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.446-556C>T		intron	N/A	ENSP00000431199.1	Q5SRN2-3
	TSBP1	ENST00000442822.6	TSL:1	c.425-556C>T		intron	N/A	ENSP00000411164.2	C9J9T8
	TSBP1	ENST00000447241.6	TSL:5	c.494-556C>T		intron	N/A	ENSP00000415517.2	Q5SRN2-1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116664 AN: 151930 Hom.: 45072 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.768 AC: 116766 AN: 152048 Hom.: 45118 Cov.: 31 AF XY: 0.775 AC XY: 57571 AN XY: 74322

African (AFR) AF: 0.712 AC: 29493 AN: 41414

American (AMR) AF: 0.760 AC: 11622 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2747 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4514 AN: 5174

South Asian (SAS) AF: 0.895 AC: 4324 AN: 4830

European-Finnish (FIN) AF: 0.865 AC: 9155 AN: 10582

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52282 AN: 67970

Other (OTH) AF: 0.753 AC: 1591 AN: 2112

Alfa AF: 0.779 Hom.: 169775

Bravo AF: 0.754

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.72
PhyloP100		-0.49
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: rs3132959; hg19: chr6-32298942;