rs17201619

Variant names:

• chr17-6210685-G-A
• rs17201619

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0158

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0625

Gnomad4 OTH AF: 0.0614

Alfa AF: 0.0658 Hom.: 878

Bravo AF: 0.0710

Asia WGS AF: 0.285 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17201619; hg19: chr17-6114005;