rs28732201

Variant names:

• chr6-32382677-G-A
• rs28732201
• ENST00000642577.1:n.169-7537G>A

Variant summary

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

The ENST00000642577.1(TSBP1-AS1):​n.169-7537G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 152,220 control chromosomes in the GnomAD database, including 64 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 0.024 (64 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0519 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.501-287G>A		intron	N/A
	TSBP1-AS1	NR_136245.1		n.302+16838G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.169-7537G>A		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.125-4304G>A		intron	N/A
	TSBP1-AS1	ENST00000645134.1		n.88-7537G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3599 AN: 152102 Hom.: 65 Cov.: 31

Gnomad AFR AF: 0.00553

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0580

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0236 AC: 3596 AN: 152220 Hom.: 64 Cov.: 31 AF XY: 0.0228 AC XY: 1695 AN XY: 74428

African (AFR) AF: 0.00551 AC: 229 AN: 41548

American (AMR) AF: 0.0126 AC: 193 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5180

South Asian (SAS) AF: 0.0575 AC: 277 AN: 4820

European-Finnish (FIN) AF: 0.0125 AC: 133 AN: 10600

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2468 AN: 67996

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0280 Hom.: 171

Bravo AF: 0.0228

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs28732201; hg19: chr6-32350454;