6-32371209-C-T

Variant names:

• chr6-32371209-C-T
• rs2073044
• NM_001286474.2:c.13+485G>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+485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,884 control chromosomes in the GnomAD database, including 3,597 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 0.21 (3597 hom., cov: 31)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.13+485G>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+485G>A		intron_variant	Intron 1 of 25	1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31892 AN: 151766 Hom.: 3595 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.210 AC: 31900 AN: 151884 Hom.: 3597 Cov.: 31 AF XY: 0.209 AC XY: 15539 AN XY: 74198

African (AFR) AF: 0.125 AC: 5182 AN: 41360

American (AMR) AF: 0.261 AC: 3989 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1241 AN: 5160

South Asian (SAS) AF: 0.224 AC: 1078 AN: 4812

European-Finnish (FIN) AF: 0.198 AC: 2090 AN: 10532

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16601 AN: 67974

Other (OTH) AF: 0.213 AC: 449 AN: 2106

Alfa AF: 0.242 Hom.: 18171

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.88
DANN	Benign	0.42
PhyloP100		-0.41
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: rs2073044; hg19: chr6-32338986;