rs9368716

chr6-32338313-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.361+666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,882 control chromosomes in the GnomAD database, including 13,242 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 0.40 (13242 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516

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 (AMR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.361+666C>T		intron_variant		ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.243-27467G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.361+666C>T		intron_variant		1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.88-51901G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60694 AN: 151764 Hom.: 13229 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.400 AC: 60725 AN: 151882 Hom.: 13242 Cov.: 31 AF XY: 0.397 AC XY: 29448 AN XY: 74214

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.433

Alfa AF: 0.452 Hom.: 5728

Bravo AF: 0.414

Asia WGS AF: 0.376 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.9
Dann	Benign	0.45

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: rs9368716; hg19: chr6-32306090;