ENST00000442822.6:c.1359+1537C>T

Variant names:

• chr6-32291750-G-A
• rs9268148
• ENST00000442822.6:c.1359+1537C>T

Variant summary

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

The ENST00000442822.6(TSBP1):​c.1359+1537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,138 control chromosomes in the GnomAD database, including 52,284 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 0.83 (52284 hom., cov: 31)
• Consequence: TSBP1 ENST00000442822.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 35 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.440+28941G>A		intron_variant	Intron 2 of 3
TSBP1-AS1	NR_136245.1	n.242+36336G>A		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1	n.242+36336G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000442822.6	c.1359+1537C>T		intron_variant	Intron 25 of 25	1		ENSP00000411164.2
TSBP1-AS1	ENST00000611838.1	n.131+36336G>A		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000642577.1	n.108+28941G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125889 AN: 152020 Hom.: 52235 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.828 AC: 125995 AN: 152138 Hom.: 52284 Cov.: 31 AF XY: 0.831 AC XY: 61816 AN XY: 74382

African (AFR) AF: 0.787 AC: 32627 AN: 41480

American (AMR) AF: 0.845 AC: 12918 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2987 AN: 3470

East Asian (EAS) AF: 0.907 AC: 4705 AN: 5190

South Asian (SAS) AF: 0.920 AC: 4439 AN: 4824

European-Finnish (FIN) AF: 0.861 AC: 9110 AN: 10586

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56365 AN: 67982

Other (OTH) AF: 0.830 AC: 1756 AN: 2116

Alfa AF: 0.836 Hom.: 183831

Bravo AF: 0.824

Asia WGS AF: 0.882 AC: 3068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		0.072
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: rs9268148; hg19: chr6-32259527;