chr6-32354616-C-T

Position:

• chr6-32354616-C-T

Variant summary

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

The NM_001286474.2(TSBP1):​c.259+508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,870 control chromosomes in the GnomAD database, including 18,594 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 0.48 (18594 hom., cov: 32)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1	NM_001286474.2	c.259+508G>A		intron_variant		ENST00000533191.6	NP_001273403.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1	ENST00000533191.6	c.259+508G>A		intron_variant		1	NM_001286474.2	ENSP00000431199.1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72365 AN: 151752 Hom.: 18579 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.477 AC: 72416 AN: 151870 Hom.: 18594 Cov.: 32 AF XY: 0.474 AC XY: 35203 AN XY: 74218

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.487

Alfa AF: 0.575 Hom.: 45143

Bravo AF: 0.472

Asia WGS AF: 0.484 AC: 1680 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.82

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: rs1265759; hg19: chr6-32322393;