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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.211

Alfa AF: 0.191 Hom.: 4501

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2328223; hg19: chr20-17845921;