6-32380368-A-G

Position:

• chr6-32380368-A-G

Variant summary

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

The NR_136244.1(TSBP1-AS1):​n.501-2596A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,918 control chromosomes in the GnomAD database, including 4,528 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 0.24 (4528 hom., cov: 32)
• Consequence: TSBP1-AS1 NR_136244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

TSBP1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1	n.501-2596A>G		intron_variant
TSBP1-AS1	NR_136245.1	n.302+14529A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSBP1-AS1	ENST00000642577.1	n.169-9846A>G		intron_variant
TSBP1-AS1	ENST00000644884.2	n.125-6613A>G		intron_variant
TSBP1-AS1	ENST00000645134.1	n.88-9846A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36178 AN: 151800 Hom.: 4529 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.238 AC: 36191 AN: 151918 Hom.: 4528 Cov.: 32 AF XY: 0.234 AC XY: 17404 AN XY: 74290

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.230

Alfa AF: 0.268 Hom.: 3149

Bravo AF: 0.252

Asia WGS AF: 0.162 AC: 563 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395157; hg19: chr6-32348145;