rs2894254

chr6-32377912-T-G

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+12073T>G 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 0.0625 in 152,274 control chromosomes in the GnomAD database, including 456 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 0.062 (456 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+12073T>G		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-5052T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-12302T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9520 AN: 152156 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0625 AC: 9517 AN: 152274 Hom.: 456 Cov.: 32 AF XY: 0.0581 AC XY: 4329 AN XY: 74452

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0283

Gnomad4 ASJ AF: 0.0380

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0923 Hom.: 563

Bravo AF: 0.0568

Asia WGS AF: 0.00433 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	6.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894254; hg19: chr6-32345689;