dbSNP rs8099917: :null (chr19-39252525-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_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

Clinical Significance

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

Conservation

PhyloP100: 1.79

Publications

1014 publications found

Variant links:

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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

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:

0.156

AC:

23785

AN:

152098

Hom.:

2231

Cov.:

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.:

AF XY:

0.153

AC XY:

11372

AN XY:

74420

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.195

AC:

13237

AN:

68000

Other (OTH)

AF:

0.174

AC:

368

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1030

2060

3091

4121

5151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.186

Hom.:

13627

Bravo

AF:

0.165

Asia WGS

AF:

0.105

AC:

367

AN:

3478

ClinVar

ClinVar submissions

Significance:drug response

Revision:reviewed by expert panel

View on ClinVar

Pathogenic

VUS

Benign

Condition

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

(source)

DANN

Benign

0.90

PhyloP100

1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over