rs2395148

Variant names:

• chr6-32353777-G-T
• rs2395148
• NM_001286474.2:c.259+1347C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.259+1347C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 151,998 control chromosomes in the GnomAD database, including 243 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 0.047 (243 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851
• Publications: 48 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 (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.259+1347C>A		intron_variant	Intron 8 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.259+1347C>A		intron_variant	Intron 8 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.0466 AC: 7073 AN: 151880 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0689

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0763

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0465 AC: 7070 AN: 151998 Hom.: 243 Cov.: 32 AF XY: 0.0495 AC XY: 3675 AN XY: 74306

African (AFR) AF: 0.0687 AC: 2855 AN: 41528

American (AMR) AF: 0.0193 AC: 295 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3466

East Asian (EAS) AF: 0.155 AC: 804 AN: 5184

South Asian (SAS) AF: 0.0593 AC: 286 AN: 4824

European-Finnish (FIN) AF: 0.0763 AC: 807 AN: 10580

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1881 AN: 67840

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0340 Hom.: 565

Bravo AF: 0.0429

Asia WGS AF: 0.0980 AC: 339 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		-0.85
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: rs2395148; hg19: chr6-32321554;