rs3117103

Variant names:

• chr6-32381780-A-T
• rs3117103
• ENST00000642577.1:n.169-8434A>T

Variant summary

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

The ENST00000642577.1(TSBP1-AS1):​n.169-8434A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 152,172 control chromosomes in the GnomAD database, including 717 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 0.093 (717 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 28 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 (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-1184A>T		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+15941A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.169-8434A>T		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.125-5201A>T		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-8434A>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14182 AN: 152054 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0932 AC: 14190 AN: 152172 Hom.: 717 Cov.: 32 AF XY: 0.0871 AC XY: 6483 AN XY: 74406

African (AFR) AF: 0.101 AC: 4192 AN: 41500

American (AMR) AF: 0.0440 AC: 673 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.0171 AC: 89 AN: 5190

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4830

European-Finnish (FIN) AF: 0.0848 AC: 899 AN: 10596

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7875 AN: 67970

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.111 Hom.: 124

Bravo AF: 0.0900

Asia WGS AF: 0.0260 AC: 92 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.70
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3117103; hg19: chr6-32349557;