rs3117106

Variant names:

• chr6-32375592-T-C
• rs3117106
• ENST00000642577.1:n.168+9753T>C

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+9753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,076 control chromosomes in the GnomAD database, including 3,805 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 0.20 (3805 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000642577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-7372T>C		intron_variant	Intron 3 of 3
TSBP1-AS1	NR_136245.1	n.302+9753T>C		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+9753T>C		intron_variant	Intron 2 of 5
TSBP1-AS1	ENST00000644884.2	n.124+9753T>C		intron_variant	Intron 2 of 3
TSBP1-AS1	ENST00000645134.1	n.88-14622T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30166 AN: 151960 Hom.: 3794 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.199 AC: 30207 AN: 152076 Hom.: 3805 Cov.: 31 AF XY: 0.191 AC XY: 14237 AN XY: 74376

African (AFR) AF: 0.361 AC: 14948 AN: 41428

American (AMR) AF: 0.136 AC: 2076 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3472

East Asian (EAS) AF: 0.132 AC: 685 AN: 5170

South Asian (SAS) AF: 0.132 AC: 634 AN: 4820

European-Finnish (FIN) AF: 0.0875 AC: 928 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9677 AN: 67972

Other (OTH) AF: 0.205 AC: 433 AN: 2114

Alfa AF: 0.186 Hom.: 787

Bravo AF: 0.210

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.63
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3117106; hg19: chr6-32343369;