chr6-32286877-A-G

Variant names:

• chr6-32286877-A-G
• rs9268132
• ENST00000611838.1:n.131+31463A>G

Variant summary

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

The ENST00000611838.1(TSBP1-AS1):​n.131+31463A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,072 control chromosomes in the GnomAD database, including 9,629 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 0.33 (9629 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 33 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.440+24068A>G		intron_variant	Intron 2 of 3
TSBP1-AS1	NR_136245.1	n.242+31463A>G		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1	n.242+31463A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000611838.1	n.131+31463A>G		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000642577.1	n.108+24068A>G		intron_variant	Intron 1 of 5
TSBP1-AS1	ENST00000644884.2	n.64+31463A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50867 AN: 151954 Hom.: 9617 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.335 AC: 50890 AN: 152072 Hom.: 9629 Cov.: 31 AF XY: 0.335 AC XY: 24896 AN XY: 74318

African (AFR) AF: 0.160 AC: 6654 AN: 41504

American (AMR) AF: 0.446 AC: 6808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1965 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1898 AN: 5172

South Asian (SAS) AF: 0.428 AC: 2064 AN: 4820

European-Finnish (FIN) AF: 0.297 AC: 3137 AN: 10560

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27119 AN: 67958

Other (OTH) AF: 0.352 AC: 745 AN: 2114

Alfa AF: 0.388 Hom.: 36390

Bravo AF: 0.340

Asia WGS AF: 0.342 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.66
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9268132; hg19: chr6-32254654;