rs539703

chr6-32320685-A-Cchr6-32320685-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):c.532+1801T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,050 control chromosomes in the GnomAD database, including 9,552 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 0.33 (9552 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.532+1801T>G		intron_variant		ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.243-45095A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.532+1801T>G		intron_variant		1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.87+65271A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50696 AN: 151932 Hom.: 9539 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.334 AC: 50725 AN: 152050 Hom.: 9552 Cov.: 31 AF XY: 0.334 AC XY: 24805 AN XY: 74316

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.347

Alfa AF: 0.377 Hom.: 5236

Bravo AF: 0.339

Asia WGS AF: 0.344 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.72

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: rs539703; hg19: chr6-32288462;