rs2322779

Variant names:

• chr17-13030629-A-G
• rs2322779

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 0.212 in 152,114 control chromosomes in the GnomAD database, including 3,797 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 0.21 (3797 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.212 AC: 32229 AN: 151994 Hom.: 3792 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.212 AC: 32263 AN: 152114 Hom.: 3797 Cov.: 33 AF XY: 0.212 AC XY: 15800 AN XY: 74370

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.231

Alfa AF: 0.184 Hom.: 347

Bravo AF: 0.221

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2322779; hg19: chr17-12933946;