rs17533090

Variant names:

• chr6-32622945-G-T
• rs17533090

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 0.16 in 151,814 control chromosomes in the GnomAD database, including 2,054 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 (2054 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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: 0.160 AC: 24203 AN: 151694 Hom.: 2049 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.160 AC: 24230 AN: 151814 Hom.: 2054 Cov.: 33 AF XY: 0.161 AC XY: 11930 AN XY: 74218

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.178

Alfa AF: 0.158 Hom.: 999

Bravo AF: 0.153

Asia WGS AF: 0.145 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17533090; hg19: chr6-32590722;