rs9368716

Variant names:

• chr6-32338313-G-A
• rs9368716
• NM_001286474.2:c.361+666C>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.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
• Publications: 26 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 (AMR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.361+666C>T		intron_variant	Intron 12 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.361+666C>T		intron_variant	Intron 12 of 25	1	NM_001286474.2	ENSP00000431199.1

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

African (AFR) AF: 0.239 AC: 9885 AN: 41386

American (AMR) AF: 0.531 AC: 8110 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3468

East Asian (EAS) AF: 0.417 AC: 2147 AN: 5148

South Asian (SAS) AF: 0.457 AC: 2193 AN: 4802

European-Finnish (FIN) AF: 0.303 AC: 3196 AN: 10540

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31524 AN: 67960

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.448 Hom.: 29031

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
PhyloP100		0.52
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: rs9368716; hg19: chr6-32306090;