chr6-32373095-C-G

Variant names:

• chr6-32373095-C-G
• rs3129944
• ENST00000642577.1:n.168+7256C>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.168+7256C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,886 control chromosomes in the GnomAD database, including 6,643 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 0.28 (6643 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 10 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.500+7256C>G		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+7256C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.168+7256C>G		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+7256C>G		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-17119C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42948 AN: 151768 Hom.: 6630 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.283 AC: 43000 AN: 151886 Hom.: 6643 Cov.: 31 AF XY: 0.282 AC XY: 20930 AN XY: 74248

African (AFR) AF: 0.396 AC: 16391 AN: 41344

American (AMR) AF: 0.236 AC: 3598 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2222 AN: 5166

South Asian (SAS) AF: 0.280 AC: 1345 AN: 4812

European-Finnish (FIN) AF: 0.250 AC: 2641 AN: 10548

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14898 AN: 67958

Other (OTH) AF: 0.288 AC: 608 AN: 2110

Alfa AF: 0.116 Hom.: 188

Bravo AF: 0.286

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs3129944; hg19: chr6-32340872;