rs3117099

chr6-32390493-G-A

Variant summary

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

The ENST00000645134.1(TSBP1-AS1):n.367G>A 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 0.277 in 154,250 control chromosomes in the GnomAD database, including 6,341 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 0.28 (6203 hom., cov: 32)
  • Exomes 𝑓: 0.22 (138 hom.)
• Consequence: TSBP1-AS1 ENST00000645134.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

HCG23 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.303-14961G>A		intron_variant, non_coding_transcript_variant
HCG23	NR_044996.1			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.367G>A		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41566 AN: 148974 Hom.: 6192 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.283

GnomAD4 exome AF: 0.222 AC: 1144 AN: 5156 Hom.: 138 Cov.: 0 AF XY: 0.220 AC XY: 610 AN XY: 2776

Gnomad4 AFR exome AF: 0.349

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.227

Gnomad4 EAS exome AF: 0.396

Gnomad4 SAS exome AF: 0.205

Gnomad4 FIN exome AF: 0.201

Gnomad4 NFE exome AF: 0.187

Gnomad4 OTH exome AF: 0.212

GnomAD4 genome AF: 0.279 AC: 41612 AN: 149094 Hom.: 6203 Cov.: 32 AF XY: 0.278 AC XY: 20242 AN XY: 72782

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.282

Alfa AF: 0.225 Hom.: 4154

Bravo AF: 0.276

Asia WGS AF: 0.371 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.7
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117099; hg19: chr6-32358270;