rs546171

Variant names:

• chr9-12879369-C-A
• rs546171

Your query was ambiguous. Multiple possible variants found:

• chr9-12879369-C-A
• chr9-12879369-C-G
• chr9-12879369-C-T

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 0.889 in 151,976 control chromosomes in the GnomAD database, including 60,227 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 0.89 (60227 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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: 0.889 AC: 134950 AN: 151858 Hom.: 60194 Cov.: 30

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.889 AC: 135032 AN: 151976 Hom.: 60227 Cov.: 30 AF XY: 0.891 AC XY: 66157 AN XY: 74280

African (AFR) AF: 0.807 AC: 33459 AN: 41462

American (AMR) AF: 0.902 AC: 13758 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3198 AN: 3470

East Asian (EAS) AF: 0.933 AC: 4822 AN: 5170

South Asian (SAS) AF: 0.837 AC: 4030 AN: 4814

European-Finnish (FIN) AF: 0.970 AC: 10287 AN: 10606

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62477 AN: 67894

Other (OTH) AF: 0.890 AC: 1876 AN: 2108

Alfa AF: 0.906 Hom.: 27519

Bravo AF: 0.881

Asia WGS AF: 0.866 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs546171; hg19: chr9-12879368;