17-65333647-A-G

Variant names:

• chr17-65333647-A-G
• rs985574

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 0.199 in 152,124 control chromosomes in the GnomAD database, including 5,135 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 0.20 (5135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30232 AN: 152006 Hom.: 5109 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.199 AC: 30318 AN: 152124 Hom.: 5135 Cov.: 32 AF XY: 0.195 AC XY: 14517 AN XY: 74388

African (AFR) AF: 0.466 AC: 19327 AN: 41448

American (AMR) AF: 0.118 AC: 1800 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 186 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5186

South Asian (SAS) AF: 0.0825 AC: 398 AN: 4826

European-Finnish (FIN) AF: 0.113 AC: 1196 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6275 AN: 67976

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.126 Hom.: 3254

Bravo AF: 0.213

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.36
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs985574; hg19: chr17-63329765;