Genetic Variant :null (chr7-2480175-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 0.143 in 152,232 control chromosomes in the GnomAD database, including 2,035 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 0.14 ( 2035 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

3 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 = 0.194 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:

0.143

AC:

21802

AN:

152114

Hom.:

2029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0469

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0588

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.143

AC:

21819

AN:

152232

Hom.:

2035

Cov.:

AF XY:

0.144

AC XY:

10705

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0469

AC:

1949

AN:

41560

American (AMR)

AF:

0.122

AC:

1858

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

396

AN:

3472

East Asian (EAS)

AF:

0.0587

AC:

304

AN:

5176

South Asian (SAS)

AF:

0.180

AC:

869

AN:

4826

European-Finnish (FIN)

AF:

0.228

AC:

2419

AN:

10604

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.197

AC:

13408

AN:

67986

Other (OTH)

AF:

0.173

AC:

364

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

931

1863

2794

3726

4657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.177

Hom.:

1345

Bravo

AF:

0.130

Asia WGS

AF:

0.137

AC:

475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

(source)

DANN

Benign

0.53

PhyloP100

-1.3

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