rs3117106

Positions:

• chr6-32375592-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.302+9753T>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 0.199 in 152,076 control chromosomes in the GnomAD database, including 3,805 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 0.20 (3805 hom., cov: 31)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+9753T>C		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-7372T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-14622T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30166 AN: 151960 Hom.: 3794 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.199 AC: 30207 AN: 152076 Hom.: 3805 Cov.: 31 AF XY: 0.191 AC XY: 14237 AN XY: 74376

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0875

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.205

Alfa AF: 0.186 Hom.: 787

Bravo AF: 0.210

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3117106; hg19: chr6-32343369;