rs3130320

Positions:

• chr6-32255481-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.242+67T>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 0.684 in 154,388 control chromosomes in the GnomAD database, including 36,478 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 0.68 (35791 hom., cov: 32)
  • Exomes 𝑓: 0.76 (687 hom.)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.242+67T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.242+67T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136246.1	n.242+67T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.87+67T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103716 AN: 151968 Hom.: 35759 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.715

GnomAD4 exome AF: 0.762 AC: 1753 AN: 2302 Hom.: 687 Cov.: 0 AF XY: 0.780 AC XY: 1012 AN XY: 1298

Gnomad4 AFR exome AF: 0.944

Gnomad4 AMR exome AF: 0.868

Gnomad4 ASJ exome AF: 0.875

Gnomad4 EAS exome AF: 0.967

Gnomad4 SAS exome AF: 0.896

Gnomad4 FIN exome AF: 0.627

Gnomad4 NFE exome AF: 0.720

Gnomad4 OTH exome AF: 0.778

GnomAD4 genome AF: 0.683 AC: 103804 AN: 152086 Hom.: 35791 Cov.: 32 AF XY: 0.683 AC XY: 50790 AN XY: 74328

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.714

Alfa AF: 0.664 Hom.: 49517

Bravo AF: 0.699

Asia WGS AF: 0.746 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130320; hg19: chr6-32223258;