Genetic Variant :null (chr22-43104206-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.405 in 152,214 control chromosomes in the GnomAD database, including 13,458 homozygotes. 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 0.40 ( 13458 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.160

Publications

119 publications found

Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

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:

0.405

AC:

61601

AN:

152096

Hom.:

13446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.548

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.488

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.475

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.416

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

GnomAD4 genome

AF:

0.405

AC:

61646

AN:

152214

Hom.:

13458

Cov.:

AF XY:

0.403

AC XY:

30011

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.247

AC:

10243

AN:

41544

American (AMR)

AF:

0.364

AC:

5567

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.488

AC:

1692

AN:

3464

East Asian (EAS)

AF:

0.316

AC:

1634

AN:

5176

South Asian (SAS)

AF:

0.426

AC:

2054

AN:

4826

European-Finnish (FIN)

AF:

0.475

AC:

5038

AN:

10600

Middle Eastern (MID)

AF:

0.537

AC:

158

AN:

294

European-Non Finnish (NFE)

AF:

0.498

AC:

33876

AN:

68004

Other (OTH)

AF:

0.419

AC:

884

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1883

3766

5650

7533

9416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<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:

0.471

Hom.:

77851

Bravo

AF:

0.390

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.9

(source)

DANN

Benign

0.58

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

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over