rs2328223

Variant names:

• chr20-17865277-A-C
• rs2328223

Your query was ambiguous. Multiple possible variants found:

• chr20-17865277-A-C
• chr20-17865277-A-G
• chr20-17865277-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 0.2 in 152,134 control chromosomes in the GnomAD database, including 3,190 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 0.20 (3190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 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: 0.200 AC: 30437 AN: 152016 Hom.: 3189 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.200 AC: 30441 AN: 152134 Hom.: 3190 Cov.: 32 AF XY: 0.204 AC XY: 15202 AN XY: 74376

African (AFR) AF: 0.176 AC: 7307 AN: 41500

American (AMR) AF: 0.238 AC: 3640 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1106 AN: 5182

South Asian (SAS) AF: 0.314 AC: 1518 AN: 4830

European-Finnish (FIN) AF: 0.218 AC: 2313 AN: 10588

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13024 AN: 67972

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.191 Hom.: 11448

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.4
DANN	Benign	0.89
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2328223; hg19: chr20-17845921;