rs3132928

Positions:

• chr6-32266238-G-A

Variant summary

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

The ENST00000611838.1(TSBP1-AS1):​n.131+10824G>A 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 151,960 control chromosomes in the GnomAD database, including 5,133 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 (5133 hom., cov: 32)
• Consequence: TSBP1-AS1 ENST00000611838.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

TSBP1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• 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/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.440+3429G>A		intron_variant
TSBP1-AS1	NR_136245.1	n.242+10824G>A		intron_variant
TSBP1-AS1	NR_136246.1	n.242+10824G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000611838.1	n.131+10824G>A		intron_variant		2
TSBP1-AS1	ENST00000642577.1	n.108+3429G>A		intron_variant
TSBP1-AS1	ENST00000644884.2	n.64+10824G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37968 AN: 151842 Hom.: 5120 Cov.: 32

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: 0.303

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.250 AC: 38014 AN: 151960 Hom.: 5133 Cov.: 32 AF XY: 0.249 AC XY: 18496 AN XY: 74288

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.231

Alfa AF: 0.232 Hom.: 1481

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	-1.0
CADD	Benign	1.1
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132928; hg19: chr6-32234015;