rs230989

Positions:

• chr17-15210118-A-G

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 0.227 in 152,044 control chromosomes in the GnomAD database, including 4,299 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 0.23 (4299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.227 AC: 34506 AN: 151926 Hom.: 4299 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.227 AC: 34497 AN: 152044 Hom.: 4299 Cov.: 31 AF XY: 0.225 AC XY: 16702 AN XY: 74324

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.250

Alfa AF: 0.264 Hom.: 7815

Bravo AF: 0.224

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230989; hg19: chr17-15113435;