rs4794067

Variant names:

• chr17-47731462-T-C
• rs4794067

Your query was ambiguous. Multiple possible variants found:

• chr17-47731462-T-C
• chr17-47731462-T-A
• chr17-47731462-T-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 0.255 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 Uncertain significance (★).

• Frequency: Genomes: 𝑓 0.26 (5265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Uncertain significance criteria provided, single submitter P:1 U:1 O:1
• Conservation: PhyloP100: -2.68
• Publications: 64 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.373 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: 0.256 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

African (AFR) AF: 0.200 AC: 8302 AN: 41464

American (AMR) AF: 0.315 AC: 4802 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3468

East Asian (EAS) AF: 0.125 AC: 649 AN: 5182

South Asian (SAS) AF: 0.387 AC: 1872 AN: 4832

European-Finnish (FIN) AF: 0.295 AC: 3113 AN: 10552

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18234 AN: 67966

Other (OTH) AF: 0.258 AC: 545 AN: 2112

Alfa AF: 0.265 Hom.: 21786

Bravo AF: 0.254

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Asthma and nasal polyps (1)
-	1	-	Immunodeficiency 88 (1)
-	-	-	Asthma, aspirin-induced, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.023
DANN	Benign	0.27
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs4794067; hg19: chr17-45808828;