chr6-32386651-A-G

Variant names:

• chr6-32386651-A-G
• rs4424066
• ENST00000642577.1:n.169-3563A>G

Variant summary

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

The NR_136245.1(TSBP1-AS1):​n.303-18803A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,016 control chromosomes in the GnomAD database, including 11,979 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 0.40 (11979 hom., cov: 31)
• Consequence: TSBP1-AS1 NR_136245.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 49 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_136245.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	NR_136245.1		n.303-18803A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1-AS1	ENST00000642577.1		n.169-3563A>G		intron	N/A
	TSBP1-AS1	ENST00000644884.2		n.125-330A>G		intron	N/A
	TSBP1-AS1	ENST00000645134.1		n.88-3563A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60090 AN: 151898 Hom.: 11979 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.395 AC: 60109 AN: 152016 Hom.: 11979 Cov.: 31 AF XY: 0.397 AC XY: 29467 AN XY: 74292

African (AFR) AF: 0.331 AC: 13737 AN: 41454

American (AMR) AF: 0.433 AC: 6614 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4814

European-Finnish (FIN) AF: 0.456 AC: 4820 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28697 AN: 67966

Other (OTH) AF: 0.388 AC: 816 AN: 2104

Alfa AF: 0.411 Hom.: 52213

Bravo AF: 0.396

Asia WGS AF: 0.318 AC: 1107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.32
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs4424066; hg19: chr6-32354428;