rs3129945

Variant names:

• chr6-32374760-G-A
• rs3129945
• ENST00000642577.1:n.168+8921G>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.168+8921G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,100 control chromosomes in the GnomAD database, including 5,821 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 0.27 (5821 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-8204G>A		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+8921G>A		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+8921G>A		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+8921G>A		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-15454G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40395 AN: 151982 Hom.: 5809 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.266 AC: 40444 AN: 152100 Hom.: 5821 Cov.: 31 AF XY: 0.263 AC XY: 19551 AN XY: 74346

African (AFR) AF: 0.377 AC: 15630 AN: 41454

American (AMR) AF: 0.225 AC: 3444 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5174

South Asian (SAS) AF: 0.179 AC: 863 AN: 4818

European-Finnish (FIN) AF: 0.250 AC: 2652 AN: 10592

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14495 AN: 67978

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.234 Hom.: 11977

Bravo AF: 0.270

Asia WGS AF: 0.301 AC: 1044 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	2.8
DANN	Benign	0.45
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3129945; hg19: chr6-32342537;