rs4877824

Variant names:

• chr9-84240944-A-G
• rs4877824

Your query was ambiguous. Multiple possible variants found:

• chr9-84240944-A-G
• chr9-84240944-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 0.555 in 151,974 control chromosomes in the GnomAD database, including 26,111 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 0.56 (26111 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.555 AC: 84279 AN: 151856 Hom.: 26039 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.555 AC: 84410 AN: 151974 Hom.: 26111 Cov.: 31 AF XY: 0.556 AC XY: 41321 AN XY: 74290

African (AFR) AF: 0.829 AC: 34353 AN: 41458

American (AMR) AF: 0.611 AC: 9326 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1635 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3198 AN: 5160

South Asian (SAS) AF: 0.499 AC: 2397 AN: 4806

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10564

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27294 AN: 67940

Other (OTH) AF: 0.540 AC: 1138 AN: 2106

Alfa AF: 0.455 Hom.: 54427

Bravo AF: 0.581

Asia WGS AF: 0.565 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.82
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4877824; hg19: chr9-86855859;