rs521446

Variant names:

• chr9-133753192-G-A
• rs521446

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 0.404 in 151,936 control chromosomes in the GnomAD database, including 13,681 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 0.40 (13681 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61435 AN: 151818 Hom.: 13680 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.404 AC: 61449 AN: 151936 Hom.: 13681 Cov.: 31 AF XY: 0.407 AC XY: 30248 AN XY: 74260

African (AFR) AF: 0.235 AC: 9728 AN: 41442

American (AMR) AF: 0.521 AC: 7951 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3468

East Asian (EAS) AF: 0.738 AC: 3816 AN: 5168

South Asian (SAS) AF: 0.475 AC: 2286 AN: 4812

European-Finnish (FIN) AF: 0.407 AC: 4291 AN: 10536

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29990 AN: 67932

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.439 Hom.: 8579

Bravo AF: 0.414

Asia WGS AF: 0.552 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs521446; hg19: chr9-136618314;