chr17-13030629-A-G

Variant names:

• chr17-13030629-A-G
• rs2322779

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 0.212 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.212 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

African (AFR) AF: 0.286 AC: 11878 AN: 41466

American (AMR) AF: 0.191 AC: 2918 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2090 AN: 5178

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1476 AN: 10588

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11067 AN: 67990

Other (OTH) AF: 0.231 AC: 488 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2322779; hg19: chr17-12933946;