rs1555115

Variant names:

• chr6-32386743-C-G
• rs1555115
• ENST00000642577.1:n.169-3471C>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.169-3471C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,156 control chromosomes in the GnomAD database, including 1,606 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 0.14 (1606 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 17 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.303-18711C>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.169-3471C>G		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.125-238C>G		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-3471C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21189 AN: 152038 Hom.: 1606 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0438

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.139 AC: 21192 AN: 152156 Hom.: 1606 Cov.: 31 AF XY: 0.143 AC XY: 10625 AN XY: 74368

African (AFR) AF: 0.131 AC: 5437 AN: 41506

American (AMR) AF: 0.129 AC: 1973 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0343 AC: 119 AN: 3472

East Asian (EAS) AF: 0.0435 AC: 226 AN: 5190

South Asian (SAS) AF: 0.0856 AC: 413 AN: 4826

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9638 AN: 67992

Other (OTH) AF: 0.138 AC: 291 AN: 2116

Alfa AF: 0.138 Hom.: 186

Bravo AF: 0.127

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1555115; hg19: chr6-32354520;