rs2416733

Variant names:

• chr9-119982452-A-C
• rs2416733

Your query was ambiguous. Multiple possible variants found:

• chr9-119982452-A-C
• chr9-119982452-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 0.459 in 152,008 control chromosomes in the GnomAD database, including 16,246 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 0.46 (16246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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: 0.460 AC: 69799 AN: 151890 Hom.: 16242 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.459 AC: 69835 AN: 152008 Hom.: 16246 Cov.: 32 AF XY: 0.461 AC XY: 34248 AN XY: 74328

African (AFR) AF: 0.505 AC: 20928 AN: 41430

American (AMR) AF: 0.505 AC: 7724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2971 AN: 5160

South Asian (SAS) AF: 0.279 AC: 1340 AN: 4804

European-Finnish (FIN) AF: 0.460 AC: 4859 AN: 10570

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28710 AN: 67968

Other (OTH) AF: 0.456 AC: 962 AN: 2110

Alfa AF: 0.420 Hom.: 7180

Bravo AF: 0.473

Asia WGS AF: 0.473 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.73
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2416733; hg19: chr9-122744730;