rs3129939

Variant names:

• chr6-32368989-A-G
• rs3129939
• NM_001286474.2:c.101-175T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.101-175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,084 control chromosomes in the GnomAD database, including 1,681 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 0.14 (1681 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 44 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.101-175T>C		intron_variant	Intron 2 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.101-175T>C		intron_variant	Intron 2 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21379 AN: 151966 Hom.: 1676 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.0835

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.141 AC: 21402 AN: 152084 Hom.: 1681 Cov.: 31 AF XY: 0.138 AC XY: 10249 AN XY: 74342

African (AFR) AF: 0.108 AC: 4464 AN: 41480

American (AMR) AF: 0.0832 AC: 1273 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3470

East Asian (EAS) AF: 0.103 AC: 533 AN: 5170

South Asian (SAS) AF: 0.132 AC: 634 AN: 4806

European-Finnish (FIN) AF: 0.188 AC: 1981 AN: 10562

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11817 AN: 67988

Other (OTH) AF: 0.133 AC: 280 AN: 2112

Alfa AF: 0.166 Hom.: 6236

Bravo AF: 0.131

Asia WGS AF: 0.143 AC: 495 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	0.014
DANN	Benign	0.61
PhyloP100		-2.6
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: rs3129939; hg19: chr6-32336766;