6-32358058-C-T

Position:

• chr6-32358058-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.218-2389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,044 control chromosomes in the GnomAD database, including 45,211 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 0.77 (45211 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.218-2389G>A		intron_variant		ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.243-7722C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.218-2389G>A		intron_variant		1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.88-32156C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116784 AN: 151926 Hom.: 45163 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.769 AC: 116888 AN: 152044 Hom.: 45211 Cov.: 30 AF XY: 0.775 AC XY: 57618 AN XY: 74332

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.754

Alfa AF: 0.781 Hom.: 32240

Bravo AF: 0.755

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.67

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: rs2894249; hg19: chr6-32325835;