rs498422

chr6-32318984-T-G

Variant summary

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

The NM_001286474.2(TSBP1):c.533-2570A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,100 control chromosomes in the GnomAD database, including 2,499 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 0.14 (2499 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

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 (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.533-2570A>C		intron_variant		ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.243-46796T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.533-2570A>C		intron_variant		1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.87+63570T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21123 AN: 151980 Hom.: 2493 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.00923

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.139 AC: 21154 AN: 152100 Hom.: 2499 Cov.: 32 AF XY: 0.136 AC XY: 10149 AN XY: 74370

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.0751

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.00923

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0746 Hom.: 1100

Bravo AF: 0.151

Asia WGS AF: 0.180 AC: 623 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	5.1
Dann	Benign	0.61

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: rs498422; hg19: chr6-32286761;