NM_001286474.2:c.260-2616C>T

Variant names:

• chr6-32352376-G-A
• rs3132963
• NM_001286474.2:c.260-2616C>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.260-2616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 151,756 control chromosomes in the GnomAD database, including 52,612 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 0.83 (52612 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 28 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 = 0.901 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	NM_001286474.2	MANE Select	c.260-2616C>T		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.260-2547C>T		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.239-2616C>T		intron	N/A	NP_001273404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.260-2616C>T		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.239-2616C>T		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.260-2547C>T		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126119 AN: 151638 Hom.: 52562 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.832 AC: 126226 AN: 151756 Hom.: 52612 Cov.: 31 AF XY: 0.835 AC XY: 61945 AN XY: 74202

African (AFR) AF: 0.788 AC: 32631 AN: 41422

American (AMR) AF: 0.847 AC: 12911 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2988 AN: 3466

East Asian (EAS) AF: 0.917 AC: 4758 AN: 5186

South Asian (SAS) AF: 0.924 AC: 4457 AN: 4824

European-Finnish (FIN) AF: 0.871 AC: 9192 AN: 10558

Middle Eastern (MID) AF: 0.874 AC: 250 AN: 286

European-Non Finnish (NFE) AF: 0.833 AC: 56452 AN: 67742

Other (OTH) AF: 0.833 AC: 1759 AN: 2112

Alfa AF: 0.849 Hom.: 63276

Bravo AF: 0.827

Asia WGS AF: 0.885 AC: 3027 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-0.10
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: rs3132963; hg19: chr6-32320153;