rs3117103

Positions:

• chr6-32381780-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.302+15941A>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 0.0932 in 152,172 control chromosomes in the GnomAD database, including 717 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 0.093 (717 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+15941A>T		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-1184A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-8434A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14182 AN: 152054 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0932 AC: 14190 AN: 152172 Hom.: 717 Cov.: 32 AF XY: 0.0871 AC XY: 6483 AN XY: 74406

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.0171

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.111 Hom.: 124

Bravo AF: 0.0900

Asia WGS AF: 0.0260 AC: 92 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117103; hg19: chr6-32349557;