rs4877822

Variant names:

• chr9-84216267-G-A
• rs4877822

Your query was ambiguous. Multiple possible variants found:

• chr9-84216267-G-A
• chr9-84216267-G-C
• chr9-84216267-G-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 0.607 in 151,984 control chromosomes in the GnomAD database, including 31,047 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 0.61 (31047 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.606 AC: 92074 AN: 151866 Hom.: 30972 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.607 AC: 92215 AN: 151984 Hom.: 31047 Cov.: 32 AF XY: 0.612 AC XY: 45461 AN XY: 74252

African (AFR) AF: 0.875 AC: 36309 AN: 41500

American (AMR) AF: 0.659 AC: 10056 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4770 AN: 5160

South Asian (SAS) AF: 0.729 AC: 3499 AN: 4800

European-Finnish (FIN) AF: 0.467 AC: 4916 AN: 10530

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29407 AN: 67942

Other (OTH) AF: 0.576 AC: 1215 AN: 2110

Alfa AF: 0.486 Hom.: 32093

Bravo AF: 0.632

Asia WGS AF: 0.843 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.53
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4877822; hg19: chr9-86831182;