rs9268403

Positions:

• chr6-32373696-T-C

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.302+7857T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,090 control chromosomes in the GnomAD database, including 4,525 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 0.24 (4525 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+7857T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.500+7857T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-16518T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36196 AN: 151972 Hom.: 4526 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.238 AC: 36209 AN: 152090 Hom.: 4525 Cov.: 32 AF XY: 0.234 AC XY: 17405 AN XY: 74346

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.230

Alfa AF: 0.264 Hom.: 3206

Bravo AF: 0.252

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268403; hg19: chr6-32341473;