rs9268494

Positions:

• chr6-32407575-A-C
• chr6-32407575-A-T

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.1865A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 154,528 control chromosomes in the GnomAD database, including 8,243 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 0.32 (8044 hom., cov: 32)
  • Exomes 𝑓: 0.35 (199 hom.)
• Consequence: TSBP1-AS1 NR_136245.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

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=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.1865A>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.2314A>C		non_coding_transcript_exon_variant	5/5
TSBP1-AS1	ENST00000642577.1	n.2395A>C		non_coding_transcript_exon_variant	6/6
TSBP1-AS1	ENST00000645167.1	n.1582A>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48542 AN: 151858 Hom.: 8042 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.320

GnomAD4 exome AF: 0.350 AC: 894 AN: 2552 Hom.: 199 Cov.: 0 AF XY: 0.344 AC XY: 467 AN XY: 1358

Gnomad4 AFR exome AF: 0.393

Gnomad4 AMR exome AF: 0.404

Gnomad4 ASJ exome AF: 0.290

Gnomad4 EAS exome AF: 0.493

Gnomad4 SAS exome AF: 0.493

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.308

Gnomad4 OTH exome AF: 0.380

GnomAD4 genome AF: 0.320 AC: 48571 AN: 151976 Hom.: 8044 Cov.: 32 AF XY: 0.320 AC XY: 23785 AN XY: 74298

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.318

Alfa AF: 0.301 Hom.: 8783

Bravo AF: 0.333

Asia WGS AF: 0.460 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	5.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268494; hg19: chr6-32375352;