rs1536482

Variant names:

• chr9-134548682-G-A
• rs1536482

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 46 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.469 AC: 19454 AN: 41442

American (AMR) AF: 0.325 AC: 4953 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5160

South Asian (SAS) AF: 0.436 AC: 2103 AN: 4820

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10578

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22526 AN: 67950

Other (OTH) AF: 0.380 AC: 803 AN: 2112

Alfa AF: 0.341 Hom.: 18325

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1536482; hg19: chr9-137440528;