rs17647258

Variant names:

• chr6-66414884-G-A
• rs17647258

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 0.0782 in 151,970 control chromosomes in the GnomAD database, including 662 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 (662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• 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 (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: 0.0783 AC: 11893 AN: 151852 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.0195

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0511

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0111

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0796

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: 0.0782 AC: 11889 AN: 151970 Hom.: 662 Cov.: 32 AF XY: 0.0780 AC XY: 5798 AN XY: 74288

African (AFR) AF: 0.0195 AC: 809 AN: 41518

American (AMR) AF: 0.0510 AC: 777 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.0111 AC: 57 AN: 5124

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10588

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.116 AC: 7893 AN: 67890

Other (OTH) AF: 0.0779 AC: 164 AN: 2104

Alfa AF: 0.0937 Hom.: 114

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	-0.82
CADD	Benign	4.5
DANN	Benign	0.66
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs17647258; hg19: chr6-67124777;