rs9268403

Variant names:

• chr6-32373696-T-C
• rs9268403
• ENST00000642577.1:n.168+7857T>C

Variant summary

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

The NR_136244.1(TSBP1-AS1):​n.500+7857T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,090 control chromosomes in the GnomAD database, including 4,525 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 0.24 (4525 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 38 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.500+7857T>C		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+7857T>C		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+7857T>C		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+7857T>C		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-16518T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36196 AN: 151972 Hom.: 4526 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.238 AC: 36209 AN: 152090 Hom.: 4525 Cov.: 32 AF XY: 0.234 AC XY: 17405 AN XY: 74346

African (AFR) AF: 0.179 AC: 7429 AN: 41500

American (AMR) AF: 0.293 AC: 4472 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3470

East Asian (EAS) AF: 0.148 AC: 767 AN: 5174

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4808

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18650 AN: 67970

Other (OTH) AF: 0.230 AC: 485 AN: 2108

Alfa AF: 0.267 Hom.: 13938

Bravo AF: 0.252

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9268403; hg19: chr6-32341473;