rs17033506

Variant names:

• chr3-35598334-G-T
• rs17033506

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 0.0284 in 152,170 control chromosomes in the GnomAD database, including 124 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 0.028 (124 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4309 AN: 152052 Hom.: 124 Cov.: 33

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00698

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0284 AC: 4321 AN: 152170 Hom.: 124 Cov.: 33 AF XY: 0.0302 AC XY: 2244 AN XY: 74396

African (AFR) AF: 0.0551 AC: 2291 AN: 41544

American (AMR) AF: 0.0172 AC: 262 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3468

East Asian (EAS) AF: 0.0653 AC: 336 AN: 5144

South Asian (SAS) AF: 0.0982 AC: 474 AN: 4828

European-Finnish (FIN) AF: 0.0350 AC: 372 AN: 10622

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00699 AC: 475 AN: 67996

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0128 Hom.: 10

Bravo AF: 0.0261

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs17033506; hg19: chr3-35639826;