17-4643264-A-G

Variant names:

• chr17-4643264-A-G
• rs9894225

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 0.706 in 151,988 control chromosomes in the GnomAD database, including 39,336 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 0.71 (39336 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107283 AN: 151870 Hom.: 39314 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.706 AC: 107340 AN: 151988 Hom.: 39336 Cov.: 31 AF XY: 0.716 AC XY: 53200 AN XY: 74308

African (AFR) AF: 0.505 AC: 20897 AN: 41394

American (AMR) AF: 0.779 AC: 11888 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2814 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5174

South Asian (SAS) AF: 0.917 AC: 4420 AN: 4822

European-Finnish (FIN) AF: 0.835 AC: 8834 AN: 10584

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51090 AN: 67964

Other (OTH) AF: 0.721 AC: 1520 AN: 2108

Alfa AF: 0.730 Hom.: 5109

Bravo AF: 0.694

Asia WGS AF: 0.917 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs9894225; hg19: chr17-4546559;