17-30566065-C-T

Variant names:

• chr17-30566065-C-T
• rs170053

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 0.468 in 152,108 control chromosomes in the GnomAD database, including 18,783 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 0.47 (18783 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.469 AC: 71255 AN: 151990 Hom.: 18787 Cov.: 34

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.468 AC: 71241 AN: 152108 Hom.: 18783 Cov.: 34 AF XY: 0.474 AC XY: 35236 AN XY: 74340

African (AFR) AF: 0.213 AC: 8838 AN: 41498

American (AMR) AF: 0.506 AC: 7739 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3468

East Asian (EAS) AF: 0.782 AC: 4041 AN: 5166

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4818

European-Finnish (FIN) AF: 0.578 AC: 6109 AN: 10566

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38425 AN: 67988

Other (OTH) AF: 0.482 AC: 1018 AN: 2114

Alfa AF: 0.507 Hom.: 2563

Bravo AF: 0.453

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.56
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs170053; hg19: chr17-28893083;