NM_001286474.2:c.13+570T>A

Variant names:

• chr6-32371124-A-T
• rs2050191
• NM_001286474.2:c.13+570T>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.13+570T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,110 control chromosomes in the GnomAD database, including 45,713 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 (45713 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.13+570T>A		intron_variant	Intron 1 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.13+570T>A		intron_variant	Intron 1 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117397 AN: 151992 Hom.: 45669 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.772 AC: 117497 AN: 152110 Hom.: 45713 Cov.: 31 AF XY: 0.780 AC XY: 57987 AN XY: 74372

African (AFR) AF: 0.718 AC: 29745 AN: 41440

American (AMR) AF: 0.762 AC: 11655 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2747 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4768 AN: 5178

South Asian (SAS) AF: 0.932 AC: 4496 AN: 4826

European-Finnish (FIN) AF: 0.865 AC: 9165 AN: 10598

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52288 AN: 67990

Other (OTH) AF: 0.755 AC: 1592 AN: 2108

Alfa AF: 0.773 Hom.: 5645

Bravo AF: 0.758

Asia WGS AF: 0.904 AC: 3146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs2050191; hg19: chr6-32338901;