dbSNP rs11594656: :null (chr10-6080046-T-A) – ACMG Classification: Benign (-13 pts)

Germline classification Cancer classification (beta)

Variant summary

Our verdict is . The variant received -13 ACMG points: 0P and 13B. BA1BP4_StrongBP6

The variant 10-6080046-T-A has been identified. The variant allele was found at a cumulative frequency of 0.183 (AC=27,791) in the gnomAD database across 152,076 control chromosomes, including 3,369 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.249. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Variant has been reported in ClinVar as Benign/Likely Benign (no review stars).

Frequency

Genomes: 𝑓 0.18 ( 3369 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1O:1

Conservation

PhyloP100: 0.206

Publications

90 publications found

Variant links:

Genome browser will be placed here

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BP6

ClinVar 0-star benign — supporting (BP6); ClinVar germline classification: Benign/Likely Benign, 0 star(s).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.2494 — 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:

0.183

AC:

27786

AN:

151958

Hom.:

3366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0514

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.0214

Gnomad SAS

AF:

0.187

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.379

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.243

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

GnomAD4 genome

AF:

0.183

AC:

27791

AN:

152076

Hom.:

3369

Cov.:

AF XY:

0.178

AC XY:

13251

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.0513

AC:

2129

AN:

41490

American (AMR)

AF:

0.228

AC:

3484

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.395

AC:

1370

AN:

3472

East Asian (EAS)

AF:

0.0214

AC:

111

AN:

5180

South Asian (SAS)

AF:

0.187

AC:

902

AN:

4814

European-Finnish (FIN)

AF:

0.169

AC:

1785

AN:

10562

Middle Eastern (MID)

AF:

0.401

AC:

117

AN:

292

European-Non Finnish (NFE)

AF:

0.253

AC:

17169

AN:

67982

Other (OTH)

AF:

0.244

AC:

516

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1086

2172

3259

4345

5431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.222

Hom.:

619

Bravo

AF:

0.182

Asia WGS

AF:

0.116

AC:

404

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.0459

AC:

5620

AN:

122568

Turkish Variome

AF:

0.263

AC:

406

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.0143

AC:

128

AN:

8960

Hom.:

ABraOM SABE-WGS-1171

AF:

0.243

AC:

568

AN:

2342

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

IL2RA-related disorder (1)

Type 1 diabetes mellitus 10 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

8.4

(source)

DANN

Benign

0.77

PhyloP100

0.21

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