rs12529049

Positions:

• chr6-32389938-C-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.303-15516C>T 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 0.144 in 152,094 control chromosomes in the GnomAD database, including 1,705 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 0.14 (1705 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

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 (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.303-15516C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-276C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21965 AN: 151976 Hom.: 1704 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.144 AC: 21973 AN: 152094 Hom.: 1705 Cov.: 32 AF XY: 0.148 AC XY: 10981 AN XY: 74350

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.141

Alfa AF: 0.132 Hom.: 2064

Bravo AF: 0.134

Asia WGS AF: 0.0740 AC: 258 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	2.8
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: rs12529049; hg19: chr6-32357715;