3-24002909-C-A

Variant names:

• chr3-24002909-C-A
• rs9883101

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 0.587 in 151,966 control chromosomes in the GnomAD database, including 26,895 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 0.59 (26895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 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: 0.587 AC: 89090 AN: 151848 Hom.: 26869 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.587 AC: 89166 AN: 151966 Hom.: 26895 Cov.: 32 AF XY: 0.585 AC XY: 43434 AN XY: 74260

African (AFR) AF: 0.446 AC: 18479 AN: 41428

American (AMR) AF: 0.625 AC: 9549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2373 AN: 3462

East Asian (EAS) AF: 0.414 AC: 2135 AN: 5158

South Asian (SAS) AF: 0.595 AC: 2869 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6188 AN: 10536

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45630 AN: 67958

Other (OTH) AF: 0.615 AC: 1297 AN: 2110

Alfa AF: 0.652 Hom.: 37701

Bravo AF: 0.582

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9883101; hg19: chr3-24044400;