Genetic Variant :null (chr9-16911759-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 classification points (ACMG Germline Pathogenicity v2019): 0P and 12B. BA1BP4_Strong

The variant 9-16911759-G-A has been identified. The variant allele was found at a cumulative frequency of 0.411 (AC=62,371) in the gnomAD database across 151,758 control chromosomes, including 13,931 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.543. 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 0.41 ( 13931 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.817

Publications

9 publications found

Variant links:

COSMIC-nc: COSV50775818

Genome browser will be placed here

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 = 0.5435 — 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:

0.411

AC:

62293

AN:

151640

Hom.:

13905

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.419

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.414

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

GnomAD4 genome

AF:

0.411

AC:

62371

AN:

151758

Hom.:

13931

Cov.:

AF XY:

0.412

AC XY:

30540

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.549

AC:

22740

AN:

41388

American (AMR)

AF:

0.532

AC:

8110

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.395

AC:

1369

AN:

3470

East Asian (EAS)

AF:

0.290

AC:

1490

AN:

5134

South Asian (SAS)

AF:

0.418

AC:

2014

AN:

4816

European-Finnish (FIN)

AF:

0.288

AC:

3030

AN:

10504

Middle Eastern (MID)

AF:

0.452

AC:

133

AN:

294

European-Non Finnish (NFE)

AF:

0.326

AC:

22133

AN:

67912

Other (OTH)

AF:

0.415

AC:

872

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1753

3505

5258

7010

8763

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<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:

0.313

Hom.:

3112

Bravo

AF:

0.434

Asia WGS

AF:

0.408

AC:

1417

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.274

AC:

33602

AN:

122756

Turkish Variome

AF:

0.334

AC:

516

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.278

AC:

2491

AN:

8960

Hom.:

359

ABraOM SABE-WGS-1171

AF:

0.405

AC:

949

AN:

2342

Hom.:

185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.17

(source)

DANN

Benign

0.61

PhyloP100

-0.82

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