rs7219669

Variant names:

• chr17-70525720-G-T
• rs7219669

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 0.458 in 151,532 control chromosomes in the GnomAD database, including 16,279 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 0.46 (16279 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.458 AC: 69408 AN: 151414 Hom.: 16267 Cov.: 29

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.458 AC: 69441 AN: 151532 Hom.: 16279 Cov.: 29 AF XY: 0.455 AC XY: 33648 AN XY: 74008

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.492

Alfa AF: 0.492 Hom.: 34184

Bravo AF: 0.468

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219669; hg19: chr17-68521861;