rs230989

Variant names:

• chr17-15210118-A-G
• rs230989

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.134 AC: 5564 AN: 41480

American (AMR) AF: 0.268 AC: 4089 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 966 AN: 3470

East Asian (EAS) AF: 0.173 AC: 896 AN: 5170

South Asian (SAS) AF: 0.147 AC: 707 AN: 4808

European-Finnish (FIN) AF: 0.276 AC: 2914 AN: 10566

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18452 AN: 67966

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.261 Hom.: 10597

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs230989; hg19: chr17-15113435;