rs7767325

Variant names:

• chr6-32266109-G-C
• rs7767325
• ENST00000611838.1:n.131+10695G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611838.1(TSBP1-AS1):​n.131+10695G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,052 control chromosomes in the GnomAD database, including 5,124 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 0.25 (5124 hom., cov: 31)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.440+3300G>C		intron_variant	Intron 2 of 3
TSBP1-AS1	NR_136245.1	n.242+10695G>C		intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1	n.242+10695G>C		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+10695G>C		intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000642577.1	n.108+3300G>C		intron_variant	Intron 1 of 5
TSBP1-AS1	ENST00000644884.2	n.64+10695G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37956 AN: 151934 Hom.: 5111 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.250 AC: 38002 AN: 152052 Hom.: 5124 Cov.: 31 AF XY: 0.249 AC XY: 18475 AN XY: 74326

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.230

Alfa AF: 0.250 Hom.: 608

Bravo AF: 0.242

Asia WGS AF: 0.238 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7767325; hg19: chr6-32233886;