6-32344305-A-G

Position:

• chr6-32344305-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.281-1047T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.76 (39227 hom., cov: 17)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TSBP1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.281-1047T>C		intron_variant		ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.281-1047T>C		intron_variant		1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 102896 AN: 136164 Hom.: 39194 Cov.: 17

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.756 AC: 102980 AN: 136276 Hom.: 39227 Cov.: 17 AF XY: 0.760 AC XY: 49670 AN XY: 65340

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.735

Alfa AF: 0.772 Hom.: 65279

Asia WGS AF: 0.753 AC: 2616 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs6904320; hg19: chr6-32312082;