dbSNP rs4942925: :null (chr13-32807106-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant 13-32807106-T-C has been identified. The variant allele was found at a cumulative frequency of 0.363 (AC=55,234) in the gnomAD database across 152,106 control chromosomes, including 10,742 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.436. 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 0.36 ( 10742 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.162

Publications

17 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 = 0.4363 — 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:

0.363

AC:

55223

AN:

151988

Hom.:

10745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.358

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.439

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.440

Gnomad OTH

AF:

0.377

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

GnomAD4 genome

AF:

0.363

AC:

55234

AN:

152106

Hom.:

10742

Cov.:

AF XY:

0.360

AC XY:

26777

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.263

AC:

10899

AN:

41498

American (AMR)

AF:

0.358

AC:

5466

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1420

AN:

3468

East Asian (EAS)

AF:

0.149

AC:

774

AN:

5184

South Asian (SAS)

AF:

0.172

AC:

829

AN:

4814

European-Finnish (FIN)

AF:

0.439

AC:

4633

AN:

10544

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.440

AC:

29949

AN:

67996

Other (OTH)

AF:

0.375

AC:

791

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1762

3523

5285

7046

8808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

528

1056

1584

2112

2640

<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:

0.410

Hom.:

21802

Bravo

AF:

0.357

Asia WGS

AF:

0.176

AC:

618

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.158

AC:

19454

AN:

122804

Turkish Variome

AF:

0.340

AC:

525

AN:

1546

Hom.:

100

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.163

AC:

1457

AN:

8960

Hom.:

123

ABraOM SABE-WGS-1171

AF:

0.391

AC:

915

AN:

2342

Hom.:

181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.9

(source)

DANN

Benign

0.74

PhyloP100

-0.16

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