rs6935269

Positions:

• chr6-32292573-T-C

Variant summary

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

The ENST00000442822.6(TSBP1):​c.1359+714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 179,170 control chromosomes in the GnomAD database, including 5,781 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 0.25 (5130 hom., cov: 32)
  • Exomes 𝑓: 0.21 (651 hom.)
• Consequence: TSBP1 ENST00000442822.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.242+37159T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.440+29764T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136246.1	n.242+37159T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.87+37159T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37969 AN: 151952 Hom.: 5117 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.206 AC: 5596 AN: 27100 Hom.: 651 AF XY: 0.202 AC XY: 2860 AN XY: 14136

Gnomad4 AFR exome AF: 0.325

Gnomad4 AMR exome AF: 0.126

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.197

Gnomad4 SAS exome AF: 0.171

Gnomad4 FIN exome AF: 0.306

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.250 AC: 38016 AN: 152070 Hom.: 5130 Cov.: 32 AF XY: 0.249 AC XY: 18487 AN XY: 74340

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.230

Alfa AF: 0.221 Hom.: 6584

Bravo AF: 0.242

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6935269; hg19: chr6-32260350;