rs8099917

Variant names:

• chr19-39252525-T-G
• rs8099917

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 0.156 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
• Clinical Significance: drug response reviewed by expert panel B:1 O:2
• Conservation: PhyloP100: 1.79
• Publications: 1008 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 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: 0.156 AC: 23785 AN: 152098 Hom.: 2231 Cov.: 32

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

African (AFR) AF: 0.0683 AC: 2839 AN: 41544

American (AMR) AF: 0.258 AC: 3944 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.0654 AC: 339 AN: 5184

South Asian (SAS) AF: 0.153 AC: 738 AN: 4820

European-Finnish (FIN) AF: 0.129 AC: 1371 AN: 10606

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13237 AN: 68000

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.186 Hom.: 13627

Bravo AF: 0.165

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: drug response

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	-	interferons, peginterferon alfa-2a, peginterferon alfa-2b, and ribavirin response - Efficacy (1)
-	-	-	peginterferon alfa-2a, peginterferon alfa-2b, ribavirin, and telaprevir response - Efficacy (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	17
DANN	Benign	0.90
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs8099917; hg19: chr19-39743165;