ENST00000642577.1:n.2323C>G

Variant names:

• chr6-32407503-C-G
• rs9268492
• ENST00000642577.1:n.2323C>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.2323C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 179,368 control chromosomes in the GnomAD database, including 8,841 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 0.31 (7360 hom., cov: 31)
  • Exomes 𝑓: 0.32 (1481 hom.)
• Consequence: TSBP1-AS1 ENST00000642577.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• 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=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1	n.1793C>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.2323C>G		non_coding_transcript_exon_variant	Exon 6 of 6
TSBP1-AS1	ENST00000645134.1	n.2242C>G		non_coding_transcript_exon_variant	Exon 5 of 5
TSBP1-AS1	ENST00000645167.1	n.1510C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46760 AN: 151854 Hom.: 7357 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.303

GnomAD4 exome AF: 0.317 AC: 8674 AN: 27396 Hom.: 1481 Cov.: 0 AF XY: 0.320 AC XY: 4600 AN XY: 14362

African (AFR) AF: 0.324 AC: 475 AN: 1464

American (AMR) AF: 0.385 AC: 1012 AN: 2630

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 302 AN: 880

East Asian (EAS) AF: 0.344 AC: 750 AN: 2182

South Asian (SAS) AF: 0.396 AC: 745 AN: 1880

European-Finnish (FIN) AF: 0.199 AC: 164 AN: 824

Middle Eastern (MID) AF: 0.304 AC: 28 AN: 92

European-Non Finnish (NFE) AF: 0.297 AC: 4739 AN: 15942

Other (OTH) AF: 0.306 AC: 459 AN: 1502

GnomAD4 genome AF: 0.308 AC: 46791 AN: 151972 Hom.: 7360 Cov.: 31 AF XY: 0.307 AC XY: 22778 AN XY: 74272

African (AFR) AF: 0.325 AC: 13446 AN: 41412

American (AMR) AF: 0.332 AC: 5066 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1852 AN: 5150

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2339 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20049 AN: 67958

Other (OTH) AF: 0.302 AC: 637 AN: 2112

Alfa AF: 0.280 Hom.: 778

Bravo AF: 0.323

Asia WGS AF: 0.378 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	2.5
DANN	Benign	0.87
PhyloP100		0.25
PromoterAI		-0.0076	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9268492; hg19: chr6-32375280;