chr6-32381934-A-G

Variant names:

• chr6-32381934-A-G
• rs9268454
• ENST00000642577.1:n.169-8280A>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.169-8280A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,154 control chromosomes in the GnomAD database, including 4,716 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 0.24 (4716 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 19 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642577.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	NR_136244.1		n.501-1030A>G		intron	N/A
	TSBP1-AS1	NR_136245.1		n.302+16095A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.169-8280A>G		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.125-5047A>G		intron	N/A
	TSBP1-AS1	ENST00000645134.1		n.88-8280A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37069 AN: 152036 Hom.: 4717 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.244 AC: 37087 AN: 152154 Hom.: 4716 Cov.: 32 AF XY: 0.239 AC XY: 17815 AN XY: 74410

African (AFR) AF: 0.198 AC: 8226 AN: 41518

American (AMR) AF: 0.295 AC: 4506 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.148 AC: 770 AN: 5188

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1970 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18671 AN: 67970

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.268 Hom.: 5198

Bravo AF: 0.258

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.65
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9268454; hg19: chr6-32349711;