rs230991

Variant names:

• chr17-15209445-C-A
• rs230991

Your query was ambiguous. Multiple possible variants found:

• chr17-15209445-C-A
• chr17-15209445-C-G

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 0.229 in 151,942 control chromosomes in the GnomAD database, including 4,355 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 (4355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34828 AN: 151824 Hom.: 4355 Cov.: 31

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.229 AC: 34820 AN: 151942 Hom.: 4355 Cov.: 31 AF XY: 0.227 AC XY: 16847 AN XY: 74230

African (AFR) AF: 0.141 AC: 5851 AN: 41464

American (AMR) AF: 0.270 AC: 4120 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.173 AC: 892 AN: 5150

South Asian (SAS) AF: 0.146 AC: 699 AN: 4800

European-Finnish (FIN) AF: 0.276 AC: 2910 AN: 10536

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18462 AN: 67948

Other (OTH) AF: 0.253 AC: 534 AN: 2110

Alfa AF: 0.236 Hom.: 2372

Bravo AF: 0.227

Asia WGS AF: 0.156 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.78
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs230991; hg19: chr17-15112762;