rs17201619

Variant names:

• chr17-6210685-G-A
• rs17201619

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 0.0695 in 151,422 control chromosomes in the GnomAD database, including 817 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 0.070 (817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.0696 AC: 10531 AN: 151306 Hom.: 822 Cov.: 31

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0695 AC: 10529 AN: 151422 Hom.: 817 Cov.: 31 AF XY: 0.0732 AC XY: 5420 AN XY: 74018

African (AFR) AF: 0.0158 AC: 647 AN: 40960

American (AMR) AF: 0.114 AC: 1732 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1866 AN: 5140

South Asian (SAS) AF: 0.252 AC: 1210 AN: 4806

European-Finnish (FIN) AF: 0.0518 AC: 547 AN: 10558

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.0625 AC: 4248 AN: 67988

Other (OTH) AF: 0.0614 AC: 129 AN: 2102

Alfa AF: 0.0652 Hom.: 1387

Bravo AF: 0.0710

Asia WGS AF: 0.285 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17201619; hg19: chr17-6114005;