dbSNP rs16996148: :null (chr19-19547663-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The variant 19-19547663-G-T has been identified. The variant allele was found at a cumulative frequency of 0.0993 (AC=15,117) in the gnomAD database across 152,240 control chromosomes, including 871 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.154. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.099 ( 871 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443

Publications

117 publications found

Variant links:

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Classification according to ACMG Germline Pathogenicity v2019

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

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.1536 — exceeds 5%% threshold (BA1 applied)

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:

0.0991

AC:

15072

AN:

152122

Hom.:

856

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.0699

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.0871

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0628

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0793

Gnomad OTH

AF:

0.0813

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0993

AC:

15117

AN:

152240

Hom.:

871

Cov.:

AF XY:

0.0983

AC XY:

7322

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.157

AC:

6510

AN:

41518

American (AMR)

AF:

0.0697

AC:

1067

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0516

AC:

179

AN:

3470

East Asian (EAS)

AF:

0.0869

AC:

449

AN:

5168

South Asian (SAS)

AF:

0.110

AC:

533

AN:

4828

European-Finnish (FIN)

AF:

0.0628

AC:

667

AN:

10620

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0793

AC:

5394

AN:

68020

Other (OTH)

AF:

0.0890

AC:

188

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

701

1401

2102

2802

3503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0865

Hom.:

2080

Bravo

AF:

0.102

Asia WGS

AF:

0.154

AC:

535

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.122

AC:

14889

AN:

121778

Turkish Variome

AF:

0.0524

AC:

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.0740

AC:

663

AN:

8960

Hom.:

ABraOM SABE-WGS-1171

AF:

0.0850

AC:

199

AN:

2342

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.9

(source)

DANN

Benign

0.71

PhyloP100

0.44

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

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over