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GeneBe

rs8099917

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1

The variant allele was found at a frequency of 0.156 in 152,216 control chromosomes in the GnomAD database, including 2,231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).

Frequency

Genomes: 𝑓 0.16 ( 2231 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

drug response reviewed by expert panel B:1O:2

Conservation

PhyloP100: 1.79
Variant links:

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ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 19-39252525-T-G is Benign according to our data. Variant chr19-39252525-T-G is described in ClinVar as [drug_response]. Clinvar id is 226027.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_benign, oryginal submissions are: {Benign=1, drug_response=2}.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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:
0.156
AC:
23785
AN:
152098
Hom.:
2231
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0682
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.258
Gnomad ASJ
AF:
0.205
Gnomad EAS
AF:
0.0650
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.129
Gnomad MID
AF:
0.237
Gnomad NFE
AF:
0.195
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23797
AN:
152216
Hom.:
2231
Cov.:
32
AF XY:
0.153
AC XY:
11372
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0683
Gnomad4 AMR
AF:
0.258
Gnomad4 ASJ
AF:
0.205
Gnomad4 EAS
AF:
0.0654
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.129
Gnomad4 NFE
AF:
0.195
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.191
Hom.:
6932
Bravo
AF:
0.165
Asia WGS
AF:
0.105
AC:
367
AN:
3478

ClinVar

Significance: drug response
Submissions summary: Benign:1Other:2
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxMar 14, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
interferons, peginterferon alfa-2a, peginterferon alfa-2b, and ribavirin response - Efficacy Other:1
drug response, reviewed by expert panelcurationPharmGKBMar 29, 2021PharmGKB Level of Evidence 1B: Level 1B clinical annotations describe variant-drug combinations with a high level of evidence supporting the association but no variant-specific prescribing guidance in an annotated clinical guideline or FDA drug label. Level 1B clinical annotations must be supported by at least two independent publications. Drug-variant association: Efficacy
peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, and telaprevir response - Efficacy Other:1
drug response, reviewed by expert panelcurationPharmGKBMar 24, 2021PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications. Drug-variant association: Efficacy

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
Cadd
Benign
17
Dann
Benign
0.90

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8099917; hg19: chr19-39743165; API