rs2894254

Variant names:

• chr6-32377912-T-G
• rs2894254
• ENST00000642577.1:n.168+12073T>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+12073T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,274 control chromosomes in the GnomAD database, including 456 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 0.062 (456 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 28 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-5052T>G		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+12073T>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+12073T>G		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.125-9069T>G		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-12302T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9520 AN: 152156 Hom.: 456 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0380

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0625 AC: 9517 AN: 152274 Hom.: 456 Cov.: 32 AF XY: 0.0581 AC XY: 4329 AN XY: 74452

African (AFR) AF: 0.0164 AC: 682 AN: 41566

American (AMR) AF: 0.0283 AC: 433 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0380 AC: 132 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.0837 AC: 887 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7224 AN: 68008

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0866 Hom.: 928

Bravo AF: 0.0568

Asia WGS AF: 0.00433 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.9
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2894254; hg19: chr6-32345689;