6-32354616-C-T

Variant names:

• chr6-32354616-C-T
• rs1265759
• NM_001286474.2:c.259+508G>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+508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,870 control chromosomes in the GnomAD database, including 18,594 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 0.48 (18594 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 37 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286474.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	NM_001286474.2	MANE Select	c.259+508G>A		intron	N/A	NP_001273403.1	A0A1U9X7D1
	TSBP1	NM_006781.5		c.259+508G>A		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.238+508G>A		intron	N/A	NP_001273404.1	E9PLW3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.259+508G>A		intron	N/A	ENSP00000431199.1	Q5SRN2-3
	TSBP1	ENST00000442822.6	TSL:1	c.238+508G>A		intron	N/A	ENSP00000411164.2	C9J9T8
	TSBP1	ENST00000447241.6	TSL:5	c.259+508G>A		intron	N/A	ENSP00000415517.2	Q5SRN2-1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72365 AN: 151752 Hom.: 18579 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.477 AC: 72416 AN: 151870 Hom.: 18594 Cov.: 32 AF XY: 0.474 AC XY: 35203 AN XY: 74218

African (AFR) AF: 0.271 AC: 11237 AN: 41430

American (AMR) AF: 0.529 AC: 8072 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2460 AN: 5184

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4824

European-Finnish (FIN) AF: 0.486 AC: 5104 AN: 10510

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38930 AN: 67880

Other (OTH) AF: 0.487 AC: 1027 AN: 2110

Alfa AF: 0.559 Hom.: 103099

Bravo AF: 0.472

Asia WGS AF: 0.484 AC: 1680 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.82
PhyloP100		-0.080
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: rs1265759; hg19: chr6-32322393;