rs9268402

chr6-32373576-G-A

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+7737G>A 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 0.45 in 151,872 control chromosomes in the GnomAD database, including 15,582 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 0.45 (15582 hom., cov: 31)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+7737G>A		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.500+7737G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-16638G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68364 AN: 151754 Hom.: 15578 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.450 AC: 68389 AN: 151872 Hom.: 15582 Cov.: 31 AF XY: 0.452 AC XY: 33569 AN XY: 74224

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.444

Alfa AF: 0.459 Hom.: 16393

Bravo AF: 0.449

Asia WGS AF: 0.413 AC: 1440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.4
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268402; hg19: chr6-32341353;