rs16824684

Variant names:

• chr3-155196301-T-G
• rs16824684

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 0.231 in 152,098 control chromosomes in the GnomAD database, including 4,320 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 0.23 (4320 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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: 0.231 AC: 35136 AN: 151980 Hom.: 4316 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.231 AC: 35164 AN: 152098 Hom.: 4320 Cov.: 33 AF XY: 0.231 AC XY: 17175 AN XY: 74360

African (AFR) AF: 0.301 AC: 12494 AN: 41498

American (AMR) AF: 0.189 AC: 2890 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.123 AC: 632 AN: 5152

South Asian (SAS) AF: 0.120 AC: 577 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2825 AN: 10568

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14415 AN: 67996

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.213 Hom.: 1858

Bravo AF: 0.227

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs16824684; hg19: chr3-154914090;