rs9391858

Variant names:

• chr6-32373621-A-G
• rs9391858
• ENST00000642577.1:n.168+7782A>G

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+7782A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,188 control chromosomes in the GnomAD database, including 1,560 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 0.13 (1560 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 47 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.500+7782A>G		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+7782A>G		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+7782A>G		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+7782A>G		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-16593A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20452 AN: 152070 Hom.: 1559 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.134 AC: 20464 AN: 152188 Hom.: 1560 Cov.: 32 AF XY: 0.138 AC XY: 10299 AN XY: 74402

African (AFR) AF: 0.0950 AC: 3946 AN: 41542

American (AMR) AF: 0.0932 AC: 1424 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.127 AC: 662 AN: 5196

South Asian (SAS) AF: 0.149 AC: 716 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2608 AN: 10570

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10270 AN: 68000

Other (OTH) AF: 0.122 AC: 256 AN: 2106

Alfa AF: 0.133 Hom.: 4831

Bravo AF: 0.119

Asia WGS AF: 0.134 AC: 470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.56
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9391858; hg19: chr6-32341398;