rs10484560

Positions:

• chr6-32330360-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.466+229C>T		intron_variant		ENST00000533191.6	NP_001273403.1
TSBP1-AS1	NR_136245.1	n.243-35420G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.466+229C>T		intron_variant		1	NM_001286474.2	ENSP00000431199	A2
TSBP1-AS1	ENST00000645134.1	n.88-59854G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0796

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0827 Hom.: 389

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484560; hg19: chr6-32298137;