chr17-17431573-A-G

Variant names:

• chr17-17431573-A-G
• rs9893203

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 0.453 in 152,064 control chromosomes in the GnomAD database, including 16,387 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 0.45 (16387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68809 AN: 151946 Hom.: 16357 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.453 AC: 68897 AN: 152064 Hom.: 16387 Cov.: 32 AF XY: 0.447 AC XY: 33220 AN XY: 74340

African (AFR) AF: 0.561 AC: 23279 AN: 41470

American (AMR) AF: 0.327 AC: 5000 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.169 AC: 877 AN: 5186

South Asian (SAS) AF: 0.423 AC: 2041 AN: 4826

European-Finnish (FIN) AF: 0.425 AC: 4490 AN: 10572

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30494 AN: 67946

Other (OTH) AF: 0.418 AC: 883 AN: 2114

Alfa AF: 0.429 Hom.: 2341

Bravo AF: 0.449

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.73
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs9893203; hg19: chr17-17334887; COSMIC: COSV69373670;