Genetic Variant :null (chr7-84896204-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 0.337 in 151,976 control chromosomes in the GnomAD database, including 9,973 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 0.34 ( 9973 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.572

Publications

0 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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:

0.337

AC:

51123

AN:

151858

Hom.:

9941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.233

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.318

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

GnomAD4 genome

AF:

0.337

AC:

51201

AN:

151976

Hom.:

9973

Cov.:

AF XY:

0.331

AC XY:

24612

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.551

AC:

22850

AN:

41472

American (AMR)

AF:

0.271

AC:

4135

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

885

AN:

3470

East Asian (EAS)

AF:

0.312

AC:

1606

AN:

5150

South Asian (SAS)

AF:

0.227

AC:

1093

AN:

4816

European-Finnish (FIN)

AF:

0.174

AC:

1842

AN:

10560

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17820

AN:

67946

Other (OTH)

AF:

0.320

AC:

671

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1671

3343

5014

6686

8357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.278

Hom.:

3324

Bravo

AF:

0.349

Asia WGS

AF:

0.275

AC:

954

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.8

(source)

DANN

Benign

0.31

PhyloP100

0.57

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