rs17647306

Variant names:

• chr6-66416954-A-G
• rs17647306

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 0.0781 in 151,768 control chromosomes in the GnomAD database, including 651 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 0.078 (651 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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: 0.0781 AC: 11851 AN: 151650 Hom.: 651 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0788

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

GnomAD4 genome AF: 0.0781 AC: 11847 AN: 151768 Hom.: 651 Cov.: 32 AF XY: 0.0778 AC XY: 5772 AN XY: 74178

African (AFR) AF: 0.0194 AC: 806 AN: 41500

American (AMR) AF: 0.0509 AC: 773 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3458

East Asian (EAS) AF: 0.0107 AC: 55 AN: 5138

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1552 AN: 10588

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7866 AN: 67760

Other (OTH) AF: 0.0780 AC: 164 AN: 2102

Alfa AF: 0.0942 Hom.: 149

Bravo AF: 0.0684

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.68
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs17647306; hg19: chr6-67126847;