Genetic Variant :null (chr11-2027906-G-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 1139 hom., cov: 4)

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

Publications

2 publications found

Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

5212

AN:

15730

Hom.:

1138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.0705

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.219

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.390

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.331

AC:

5214

AN:

15766

Hom.:

1139

Cov.:

AF XY:

0.321

AC XY:

2259

AN XY:

7040

show subpopulations

African (AFR)

AF:

0.355

AC:

1300

AN:

3658

American (AMR)

AF:

0.250

AC:

539

AN:

2160

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

133

AN:

372

East Asian (EAS)

AF:

0.0714

AC:

AN:

476

South Asian (SAS)

AF:

0.285

AC:

AN:

130

European-Finnish (FIN)

AF:

0.292

AC:

475

AN:

1624

Middle Eastern (MID)

AF:

0.219

AC:

AN:

European-Non Finnish (NFE)

AF:

0.367

AC:

2615

AN:

7124

Other (OTH)

AF:

0.399

AC:

AN:

148

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

151

302

452

603

754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

136

170

<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:

0.171

Hom.:

362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

6.2

(source)

DANN

Benign

0.14

PhyloP100

-2.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over