17-3559573-T-C

Variant names:

• chr17-3559573-T-C
• rs4790520

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 0.228 in 151,958 control chromosomes in the GnomAD database, including 4,699 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 0.23 (4699 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 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: 0.229 AC: 34705 AN: 151840 Hom.: 4700 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.228 AC: 34717 AN: 151958 Hom.: 4699 Cov.: 31 AF XY: 0.239 AC XY: 17737 AN XY: 74256

African (AFR) AF: 0.118 AC: 4895 AN: 41484

American (AMR) AF: 0.329 AC: 5027 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2494 AN: 5134

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3726 AN: 10552

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15604 AN: 67906

Other (OTH) AF: 0.256 AC: 541 AN: 2114

Alfa AF: 0.239 Hom.: 8810

Bravo AF: 0.227

Asia WGS AF: 0.363 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.38
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs4790520; hg19: chr17-3462867;