17-66816080-G-A

Variant names:

• chr17-66816080-G-A
• rs12603061

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 0.486 in 152,120 control chromosomes in the GnomAD database, including 18,621 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 0.49 (18621 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73906 AN: 152002 Hom.: 18599 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.486 AC: 73973 AN: 152120 Hom.: 18621 Cov.: 33 AF XY: 0.496 AC XY: 36871 AN XY: 74344

African (AFR) AF: 0.463 AC: 19204 AN: 41488

American (AMR) AF: 0.467 AC: 7131 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4663 AN: 5178

South Asian (SAS) AF: 0.630 AC: 3040 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6203 AN: 10562

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.456 AC: 31043 AN: 68006

Other (OTH) AF: 0.466 AC: 983 AN: 2110

Alfa AF: 0.454 Hom.: 28778

Bravo AF: 0.477

Asia WGS AF: 0.729 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.38
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs12603061; hg19: chr17-64812198;