rs3129933

Variant names:

• chr6-32368384-G-A
• rs3129933
• NM_001286474.2:c.133+398C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-32368384-G-A
• chr6-32368384-G-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.133+398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,050 control chromosomes in the GnomAD database, including 1,495 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 0.13 (1495 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 22 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.133+398C>T		intron_variant	Intron 3 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.133+398C>T		intron_variant	Intron 3 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19795 AN: 151932 Hom.: 1492 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.130 AC: 19811 AN: 152050 Hom.: 1495 Cov.: 32 AF XY: 0.126 AC XY: 9354 AN XY: 74324

African (AFR) AF: 0.103 AC: 4284 AN: 41448

American (AMR) AF: 0.0695 AC: 1061 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5182

South Asian (SAS) AF: 0.0986 AC: 475 AN: 4816

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10558

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11547 AN: 67992

Other (OTH) AF: 0.117 AC: 248 AN: 2112

Alfa AF: 0.157 Hom.: 4225

Bravo AF: 0.122

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.76
PhyloP100		-0.68
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: rs3129933; hg19: chr6-32336161;