6-32289789-G-A

Variant names:

• chr6-32289789-G-A
• rs926070
• ENST00000442822.6:c.1360-1120C>T

Variant summary

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

The ENST00000442822.6(TSBP1):​c.1360-1120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,732 control chromosomes in the GnomAD database, including 35,800 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 0.69 (35800 hom., cov: 31)
• Consequence: TSBP1 ENST00000442822.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 58 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.440+26980G>A		intron_variant	Intron 2 of 3
TSBP1-AS1	NR_136245.1	n.242+34375G>A		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1	n.242+34375G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000442822.6	c.1360-1120C>T		intron_variant	Intron 25 of 25	1		ENSP00000411164.2
TSBP1-AS1	ENST00000611838.1	n.131+34375G>A		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000642577.1	n.108+26980G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103921 AN: 151614 Hom.: 35766 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.685 AC: 104004 AN: 151732 Hom.: 35800 Cov.: 31 AF XY: 0.684 AC XY: 50716 AN XY: 74154

African (AFR) AF: 0.688 AC: 28382 AN: 41248

American (AMR) AF: 0.671 AC: 10238 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2598 AN: 3466

East Asian (EAS) AF: 0.767 AC: 3951 AN: 5152

South Asian (SAS) AF: 0.816 AC: 3925 AN: 4810

European-Finnish (FIN) AF: 0.611 AC: 6427 AN: 10526

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46129 AN: 67958

Other (OTH) AF: 0.691 AC: 1457 AN: 2108

Alfa AF: 0.696 Hom.: 149345

Bravo AF: 0.688

Asia WGS AF: 0.755 AC: 2627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.1
DANN	Benign	0.43
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs926070; hg19: chr6-32257566;