rs17604706

Variant names:

• chr5-30936726-C-T
• rs17604706

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 0.306 in 151,942 control chromosomes in the GnomAD database, including 7,651 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 0.31 (7651 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 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: 0.306 AC: 46482 AN: 151824 Hom.: 7648 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.306 AC: 46485 AN: 151942 Hom.: 7651 Cov.: 33 AF XY: 0.307 AC XY: 22792 AN XY: 74226

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.326

Alfa AF: 0.349 Hom.: 4246

Bravo AF: 0.292

Asia WGS AF: 0.272 AC: 944 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17604706; hg19: chr5-30936833;