Genetic Variant :null (chr7-83888815-G-A) – 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 0.366 in 151,682 control chromosomes in the GnomAD database, including 11,241 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 0.37 ( 11241 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10

Publications

1 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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:

0.366

AC:

55525

AN:

151562

Hom.:

11228

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.357

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

GnomAD4 genome

AF:

0.366

AC:

55564

AN:

151682

Hom.:

11241

Cov.:

AF XY:

0.372

AC XY:

27588

AN XY:

74116

show subpopulations

African (AFR)

AF:

0.210

AC:

8686

AN:

41414

American (AMR)

AF:

0.429

AC:

6520

AN:

15212

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1523

AN:

3464

East Asian (EAS)

AF:

0.134

AC:

686

AN:

5116

South Asian (SAS)

AF:

0.357

AC:

1716

AN:

4810

European-Finnish (FIN)

AF:

0.539

AC:

5678

AN:

10542

Middle Eastern (MID)

AF:

0.414

AC:

120

AN:

290

European-Non Finnish (NFE)

AF:

0.436

AC:

29557

AN:

67826

Other (OTH)

AF:

0.359

AC:

754

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1726

3453

5179

6906

8632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.408

Hom.:

41298

Bravo

AF:

0.352

Asia WGS

AF:

0.225

AC:

784

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.12

(source)

DANN

Benign

0.46

PhyloP100

-1.1

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