rs1536482

Variant names:

• chr9-134548682-G-A
• rs1536482

Variant summary

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

The variant allele was found at a frequency of 0.361 in 151,994 control chromosomes in the GnomAD database, including 10,402 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 0.36 (10402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54784 AN: 151874 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.361 AC: 54834 AN: 151994 Hom.: 10402 Cov.: 32 AF XY: 0.355 AC XY: 26404 AN XY: 74302

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.380

Alfa AF: 0.344 Hom.: 4389

Bravo AF: 0.370

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536482; hg19: chr9-137440528;