Genetic Variant :null (chr3-39541433-C-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 3-39541433-C-T has been identified. The variant allele was found at a cumulative frequency of 0.613 (AC=93,112) in the gnomAD database across 151,952 control chromosomes, including 32,365 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.765. 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 0.61 ( 32365 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.881

Publications

3 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 = 0.7646 — 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:

0.613

AC:

93117

AN:

151836

Hom.:

32369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.905

Gnomad AMR

AF:

0.679

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.631

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

GnomAD4 genome

AF:

0.613

AC:

93112

AN:

151952

Hom.:

32365

Cov.:

AF XY:

0.616

AC XY:

45753

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.259

AC:

10720

AN:

41376

American (AMR)

AF:

0.679

AC:

10356

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2503

AN:

3468

East Asian (EAS)

AF:

0.622

AC:

3214

AN:

5164

South Asian (SAS)

AF:

0.684

AC:

3290

AN:

4812

European-Finnish (FIN)

AF:

0.787

AC:

8320

AN:

10574

Middle Eastern (MID)

AF:

0.646

AC:

190

AN:

294

European-Non Finnish (NFE)

AF:

0.770

AC:

52365

AN:

67994

Other (OTH)

AF:

0.631

AC:

1329

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1469

2938

4406

5875

7344

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

752

1504

2256

3008

3760

<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:

0.733

Hom.:

24596

Bravo

AF:

0.588

Asia WGS

AF:

0.611

AC:

2126

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.615

AC:

75389

AN:

122604

Turkish Variome

AF:

0.761

AC:

1177

AN:

1546

Hom.:

447

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.630

AC:

5643

AN:

8960

Hom.:

1771

ABraOM SABE-WGS-1171

AF:

0.638

AC:

1494

AN:

2342

Hom.:

503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.44

(source)

DANN

Benign

0.58

PhyloP100

-0.88

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