rs3129945

chr6-32374760-G-A

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+8921G>A 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 0.266 in 152,100 control chromosomes in the GnomAD database, including 5,821 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 0.27 (5821 hom., cov: 31)
• Consequence: TSBP1-AS1 NR_136245.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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 (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSBP1-AS1	NR_136245.1	n.302+8921G>A		intron_variant, non_coding_transcript_variant
TSBP1-AS1	NR_136244.1	n.501-8204G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSBP1-AS1	ENST00000645134.1	n.88-15454G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40395 AN: 151982 Hom.: 5809 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.266 AC: 40444 AN: 152100 Hom.: 5821 Cov.: 31 AF XY: 0.263 AC XY: 19551 AN XY: 74346

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.270

Alfa AF: 0.224 Hom.: 2938

Bravo AF: 0.270

Asia WGS AF: 0.301 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.8
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129945; hg19: chr6-32342537;