rs10484560

Variant names:

• chr6-32330360-G-A
• rs10484560
• NM_001286474.2:c.466+229C>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.466+229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,024 control chromosomes in the GnomAD database, including 798 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 0.086 (798 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 23 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 (EAS) allele frequency at 95% confidence interval = 0.0933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.466+229C>T		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+229C>T		intron_variant	Intron 17 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13079 AN: 151906 Hom.: 794 Cov.: 31

Gnomad AFR AF: 0.0383

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0791

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0862 AC: 13098 AN: 152024 Hom.: 798 Cov.: 31 AF XY: 0.0940 AC XY: 6984 AN XY: 74292

African (AFR) AF: 0.0384 AC: 1593 AN: 41490

American (AMR) AF: 0.0905 AC: 1382 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3470

East Asian (EAS) AF: 0.100 AC: 519 AN: 5168

South Asian (SAS) AF: 0.0796 AC: 383 AN: 4814

European-Finnish (FIN) AF: 0.255 AC: 2679 AN: 10510

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0900 AC: 6120 AN: 67992

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0812 Hom.: 554

Bravo AF: 0.0699

Asia WGS AF: 0.101 AC: 351 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.46
PhyloP100		0.16
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: rs10484560; hg19: chr6-32298137;