rs3129900

Variant names:

• chr6-32338202-G-T
• rs3129900
• NM_001286474.2:c.361+777C>A

Variant summary

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

The NM_001286474.2(TSBP1):​c.361+777C>A 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 152,142 control chromosomes in the GnomAD database, including 52,772 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 (52772 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 58 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.361+777C>A		intron_variant	Intron 12 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.361+777C>A		intron_variant	Intron 12 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126469 AN: 152024 Hom.: 52722 Cov.: 30

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.834

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: 126575 AN: 152142 Hom.: 52772 Cov.: 30 AF XY: 0.835 AC XY: 62110 AN XY: 74376

African (AFR) AF: 0.788 AC: 32674 AN: 41468

American (AMR) AF: 0.847 AC: 12950 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2991 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4757 AN: 5182

South Asian (SAS) AF: 0.924 AC: 4454 AN: 4820

European-Finnish (FIN) AF: 0.871 AC: 9225 AN: 10590

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56680 AN: 67998

Other (OTH) AF: 0.833 AC: 1760 AN: 2114

Alfa AF: 0.839 Hom.: 119726

Bravo AF: 0.827

Asia WGS AF: 0.885 AC: 3078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.74
PhyloP100		0.53
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: rs3129900; hg19: chr6-32305979;