rs9268402

Variant names:

• chr6-32373576-G-A
• rs9268402
• ENST00000642577.1:n.168+7737G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642577.1(TSBP1-AS1):​n.168+7737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,872 control chromosomes in the GnomAD database, including 15,582 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 0.45 (15582 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 58 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.500+7737G>A		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+7737G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.168+7737G>A		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+7737G>A		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-16638G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68364 AN: 151754 Hom.: 15578 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.450 AC: 68389 AN: 151872 Hom.: 15582 Cov.: 31 AF XY: 0.452 AC XY: 33569 AN XY: 74224

African (AFR) AF: 0.392 AC: 16209 AN: 41374

American (AMR) AF: 0.465 AC: 7103 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1420 AN: 3466

East Asian (EAS) AF: 0.407 AC: 2103 AN: 5164

South Asian (SAS) AF: 0.527 AC: 2541 AN: 4822

European-Finnish (FIN) AF: 0.506 AC: 5330 AN: 10540

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32050 AN: 67918

Other (OTH) AF: 0.444 AC: 937 AN: 2110

Alfa AF: 0.457 Hom.: 44367

Bravo AF: 0.449

Asia WGS AF: 0.413 AC: 1440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.4
DANN	Benign	0.31
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs9268402; hg19: chr6-32341353;