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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.606 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

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.576

Alfa AF: 0.469 Hom.: 23051

Bravo AF: 0.632

Asia WGS AF: 0.843 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877822; hg19: chr9-86831182;