rs9891572

Positions:

• chr17-2525214-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 0.176 in 152,054 control chromosomes in the GnomAD database, including 2,419 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 0.18 (2419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26684 AN: 151936 Hom.: 2417 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.176 AC: 26716 AN: 152054 Hom.: 2419 Cov.: 32 AF XY: 0.177 AC XY: 13148 AN XY: 74310

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.174

Alfa AF: 0.162 Hom.: 3403

Bravo AF: 0.179

Asia WGS AF: 0.287 AC: 996 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	5.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9891572; hg19: chr17-2428508;