dbSNP rs2872507: :null (chr17-39884510-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 17-39884510-G-A has been identified. The variant allele was found at a cumulative frequency of 0.389 (AC=59,173) in the gnomAD database across 152,006 control chromosomes, including 12,248 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.447. 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 0.39 ( 12248 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.354

Publications

185 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 = 0.4473 — 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:

0.389

AC:

59125

AN:

151888

Hom.:

12236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.661

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.389

AC:

59173

AN:

152006

Hom.:

12248

Cov.:

AF XY:

0.392

AC XY:

29125

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.261

AC:

10801

AN:

41462

American (AMR)

AF:

0.391

AC:

5971

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.416

AC:

1443

AN:

3466

East Asian (EAS)

AF:

0.270

AC:

1397

AN:

5178

South Asian (SAS)

AF:

0.371

AC:

1790

AN:

4826

European-Finnish (FIN)

AF:

0.532

AC:

5596

AN:

10528

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30683

AN:

67950

Other (OTH)

AF:

0.374

AC:

788

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1799

3599

5398

7198

8997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.427

Hom.:

62476

Bravo

AF:

0.367

Asia WGS

AF:

0.370

AC:

1286

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.265

AC:

32464

AN:

122598

Turkish Variome

AF:

0.403

AC:

623

AN:

1546

Hom.:

125

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.247

AC:

2213

AN:

8960

Hom.:

270

ABraOM SABE-WGS-1171

AF:

0.358

AC:

838

AN:

2342

Hom.:

145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

1.0

(source)

DANN

Benign

0.68

PhyloP100

-0.35

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