rs888219

Variant names:

• chr9-126166744-A-C
• rs888219

Your query was ambiguous. Multiple possible variants found:

• chr9-126166744-A-C
• chr9-126166744-A-G
• chr9-126166744-A-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 0.763 in 152,080 control chromosomes in the GnomAD database, including 44,602 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 0.76 (44602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116062 AN: 151962 Hom.: 44594 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.763 AC: 116113 AN: 152080 Hom.: 44602 Cov.: 32 AF XY: 0.761 AC XY: 56551 AN XY: 74332

African (AFR) AF: 0.695 AC: 28848 AN: 41482

American (AMR) AF: 0.745 AC: 11385 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2889 AN: 3472

East Asian (EAS) AF: 0.661 AC: 3400 AN: 5146

South Asian (SAS) AF: 0.857 AC: 4130 AN: 4820

European-Finnish (FIN) AF: 0.713 AC: 7540 AN: 10568

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55335 AN: 67990

Other (OTH) AF: 0.775 AC: 1636 AN: 2112

Alfa AF: 0.796 Hom.: 160265

Bravo AF: 0.759

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.4
DANN	Benign	0.76
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs888219; hg19: chr9-128929023;