NM_001286474.2:c.532+2073A>G

Variant names:

• chr6-32320413-T-C
• rs574710
• NM_001286474.2:c.532+2073A>G

Variant summary

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

The NM_001286474.2(TSBP1):​c.532+2073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,946 control chromosomes in the GnomAD database, including 9,987 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 0.34 (9987 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 22 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.532+2073A>G		intron_variant	Intron 20 of 25	ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.532+2073A>G		intron_variant	Intron 20 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51808 AN: 151828 Hom.: 9975 Cov.: 30

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.341 AC: 51841 AN: 151946 Hom.: 9987 Cov.: 30 AF XY: 0.342 AC XY: 25412 AN XY: 74254

African (AFR) AF: 0.162 AC: 6719 AN: 41488

American (AMR) AF: 0.459 AC: 6994 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1976 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2008 AN: 5158

South Asian (SAS) AF: 0.440 AC: 2107 AN: 4788

European-Finnish (FIN) AF: 0.322 AC: 3402 AN: 10560

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27365 AN: 67930

Other (OTH) AF: 0.365 AC: 768 AN: 2102

Alfa AF: 0.393 Hom.: 13716

Bravo AF: 0.345

Asia WGS AF: 0.397 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.34
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: rs574710; hg19: chr6-32288190; COSMIC: COSV66659837; COSMIC: COSV66659837;