rs7219669

Positions:

• chr17-70525720-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;