rs6906662

Variant names:

• chr6-32298729-G-A
• rs6906662
• NM_001286474.2:c.631+1193C>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.631+1193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 152,294 control chromosomes in the GnomAD database, including 409 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 0.068 (409 hom., cov: 33)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 23 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.631+1193C>T		intron_variant	Intron 25 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.631+1193C>T		intron_variant	Intron 25 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10347 AN: 152176 Hom.: 407 Cov.: 33

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0402

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0144

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0680 AC: 10359 AN: 152294 Hom.: 409 Cov.: 33 AF XY: 0.0679 AC XY: 5056 AN XY: 74468

African (AFR) AF: 0.0891 AC: 3705 AN: 41568

American (AMR) AF: 0.0402 AC: 615 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.0144 AC: 75 AN: 5192

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4824

European-Finnish (FIN) AF: 0.0767 AC: 814 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4306 AN: 68010

Other (OTH) AF: 0.0695 AC: 147 AN: 2116

Alfa AF: 0.0595 Hom.: 512

Bravo AF: 0.0657

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		0.081
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: rs6906662; hg19: chr6-32266506;