17-31779568-G-A

Variant names:

• chr17-31779568-G-A
• rs8082305

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 0.153 in 151,726 control chromosomes in the GnomAD database, including 1,886 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 0.15 (1886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23125 AN: 151608 Hom.: 1884 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.153 AC: 23145 AN: 151726 Hom.: 1886 Cov.: 32 AF XY: 0.152 AC XY: 11264 AN XY: 74158

African (AFR) AF: 0.174 AC: 7184 AN: 41256

American (AMR) AF: 0.0942 AC: 1440 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3466

East Asian (EAS) AF: 0.146 AC: 754 AN: 5168

South Asian (SAS) AF: 0.0738 AC: 355 AN: 4812

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10347 AN: 67876

Other (OTH) AF: 0.153 AC: 322 AN: 2098

Alfa AF: 0.152 Hom.: 2544

Bravo AF: 0.150

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs8082305; hg19: chr17-30106587;