17-47731462-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The variant allele was found at a frequency of 0.255 in 152,046 control chromosomes in the GnomAD database, including 5,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic,risk factor (no stars).

• Frequency: Genomes: 𝑓 0.26 (5265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Pathogenic; risk factor no assertion criteria provided P:1 O:1
• Conservation: PhyloP100: -2.68

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 17-47731462-T-C is Pathogenic according to our data. Variant chr17-47731462-T-C is described in ClinVar as [Pathogenic, risk_factor]. Clinvar id is 5321.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).. Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.373 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: 0.256 AC: 38827 AN: 151928 Hom.: 5268 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.255 AC: 38843 AN: 152046 Hom.: 5265 Cov.: 32 AF XY: 0.260 AC XY: 19291 AN XY: 74320

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.258

Alfa AF: 0.273 Hom.: 9343

Bravo AF: 0.254

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Significance: Pathogenic; risk factor

Submissions summary: Pathogenic:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Asthma and nasal polyps Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 01, 2005

- -

Asthma, aspirin-induced, susceptibility to Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jun 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.023
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4794067; hg19: chr17-45808828;