dbSNP rs614367: :null (chr11-69513996-C-T) – 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 11-69513996-C-T has been identified. The variant allele was found at a cumulative frequency of 0.135 (AC=20,512) in the gnomAD database across 152,136 control chromosomes, including 1,512 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.153. 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 0.13 ( 1512 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.867

Publications

109 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 = 0.1533 — 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:

0.135

AC:

20500

AN:

152018

Hom.:

1512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.0890

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.00830

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.121

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.135

AC:

20512

AN:

152136

Hom.:

1512

Cov.:

AF XY:

0.136

AC XY:

10132

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.128

AC:

5332

AN:

41512

American (AMR)

AF:

0.0889

AC:

1357

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

521

AN:

3472

East Asian (EAS)

AF:

0.00793

AC:

AN:

5170

South Asian (SAS)

AF:

0.163

AC:

785

AN:

4824

European-Finnish (FIN)

AF:

0.174

AC:

1843

AN:

10580

Middle Eastern (MID)

AF:

0.110

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.151

AC:

10241

AN:

68000

Other (OTH)

AF:

0.134

AC:

282

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

918

1836

2754

3672

4590

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.140

Hom.:

7311

Bravo

AF:

0.124

Asia WGS

AF:

0.108

AC:

374

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.000938

AC:

115

AN:

122650

Turkish Variome

AF:

0.134

AC:

207

AN:

1544

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.00725

AC:

AN:

8960

Hom.:

ABraOM SABE-WGS-1171

AF:

0.123

AC:

289

AN:

2342

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.8

(source)

DANN

Benign

0.35

PhyloP100

-0.87

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