17-47731462-T-C

Variant names:

• chr17-47731462-T-C
• rs4794067

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Jun 01, 2005

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Asthma, aspirin-induced, susceptibility to Other:1

Jun 01, 2005

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;