6-32292782-A-G

Position:

• chr6-32292782-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.*199T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 535,074 control chromosomes in the GnomAD database, including 41,925 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 0.33 (9627 hom., cov: 32)
  • Exomes 𝑓: 0.40 (32298 hom.)
• Consequence: TSBP1 NM_001286474.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1	NM_001286474.2	c.*199T>C		3_prime_UTR_variant	26/26	ENST00000533191.6
TSBP1-AS1	NR_136245.1	n.242+37368A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1	ENST00000533191.6	c.*199T>C		3_prime_UTR_variant	26/26	1	NM_001286474.2	A2
TSBP1-AS1	ENST00000645134.1	n.87+37368A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50863 AN: 152010 Hom.: 9615 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.356

GnomAD4 exome AF: 0.400 AC: 153327 AN: 382946 Hom.: 32298 Cov.: 3 AF XY: 0.406 AC XY: 81412 AN XY: 200590

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.488

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.309

Gnomad4 SAS exome AF: 0.461

Gnomad4 FIN exome AF: 0.309

Gnomad4 NFE exome AF: 0.412

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.335 AC: 50891 AN: 152128 Hom.: 9627 Cov.: 32 AF XY: 0.335 AC XY: 24887 AN XY: 74366

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.352

Alfa AF: 0.388 Hom.: 4996

Bravo AF: 0.340

Asia WGS AF: 0.343 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.65

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: rs482194; hg19: chr6-32260559;