rs4877822

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;