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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.764 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

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.775

Alfa AF: 0.801 Hom.: 73662

Bravo AF: 0.759

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs888219; hg19: chr9-128929023;