6-32330124-A-G

Variant names:

• chr6-32330124-A-G
• rs3132958
• NM_001286474.2:c.466+465T>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.466+465T>C 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 151,760 control chromosomes in the GnomAD database, including 45,036 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 (45036 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 29 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.466+465T>C		intron_variant	Intron 17 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.466+465T>C		intron_variant	Intron 17 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116454 AN: 151642 Hom.: 44988 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.768 AC: 116558 AN: 151760 Hom.: 45036 Cov.: 31 AF XY: 0.774 AC XY: 57444 AN XY: 74176

African (AFR) AF: 0.713 AC: 29492 AN: 41338

American (AMR) AF: 0.761 AC: 11596 AN: 15242

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

East Asian (EAS) AF: 0.871 AC: 4470 AN: 5130

South Asian (SAS) AF: 0.896 AC: 4325 AN: 4828

European-Finnish (FIN) AF: 0.865 AC: 9124 AN: 10554

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

European-Non Finnish (NFE) AF: 0.769 AC: 52179 AN: 67880

Other (OTH) AF: 0.752 AC: 1589 AN: 2112

Alfa AF: 0.778 Hom.: 172353

Bravo AF: 0.755

Asia WGS AF: 0.855 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-1.3
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: rs3132958; hg19: chr6-32297901;