17-65307301-C-T

Variant names:

• chr17-65307301-C-T
• rs724560

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 0.292 in 152,120 control chromosomes in the GnomAD database, including 7,215 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 0.29 (7215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44292 AN: 152002 Hom.: 7199 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.292 AC: 44356 AN: 152120 Hom.: 7215 Cov.: 33 AF XY: 0.285 AC XY: 21174 AN XY: 74368

African (AFR) AF: 0.415 AC: 17226 AN: 41484

American (AMR) AF: 0.223 AC: 3407 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3468

East Asian (EAS) AF: 0.0291 AC: 151 AN: 5182

South Asian (SAS) AF: 0.181 AC: 873 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2689 AN: 10578

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18251 AN: 67980

Other (OTH) AF: 0.299 AC: 633 AN: 2114

Alfa AF: 0.306 Hom.: 1341

Bravo AF: 0.296

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs724560; hg19: chr17-63303419;