rs17530479

Variant names:

• chr19-33369130-G-T
• rs17530479

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.155 in 152,174 control chromosomes in the GnomAD database, including 2,178 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 0.16 (2178 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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: 0.155 AC: 23638 AN: 152056 Hom.: 2170 Cov.: 32

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0571

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.155 AC: 23663 AN: 152174 Hom.: 2178 Cov.: 32 AF XY: 0.155 AC XY: 11552 AN XY: 74404

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0582

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.184

Alfa AF: 0.171 Hom.: 324

Bravo AF: 0.160

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17530479; hg19: chr19-33860036;