rs9268005

Variant names:

• chr6-32256611-C-A
• rs9268005
• ENST00000425033.1:n.231+670C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32256611-C-A
• chr6-32256611-C-G
• chr6-32256611-C-T

Variant summary

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

The ENST00000425033.1(TSBP1-AS1):​n.231+670C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,940 control chromosomes in the GnomAD database, including 35,807 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 0.69 (35807 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000425033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 18 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.242+1197C>A		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136245.1	n.242+1197C>A		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1	n.242+1197C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000425033.1	n.231+670C>A		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000611838.1	n.131+1197C>A		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000644884.2	n.64+1197C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103996 AN: 151822 Hom.: 35773 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.685 AC: 104079 AN: 151940 Hom.: 35807 Cov.: 32 AF XY: 0.683 AC XY: 50754 AN XY: 74258

African (AFR) AF: 0.686 AC: 28408 AN: 41390

American (AMR) AF: 0.671 AC: 10248 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2603 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3980 AN: 5184

South Asian (SAS) AF: 0.816 AC: 3937 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6404 AN: 10510

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46144 AN: 67974

Other (OTH) AF: 0.691 AC: 1458 AN: 2110

Alfa AF: 0.694 Hom.: 31379

Bravo AF: 0.688

Asia WGS AF: 0.753 AC: 2619 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.46
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs9268005; hg19: chr6-32224388;