rs17604706

chr5-30936726-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;