Genetic Variant :null (chr4-27450860-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 0.216 in 152,054 control chromosomes in the GnomAD database, including 4,428 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 0.22 ( 4428 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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:

0.216

AC:

32842

AN:

151936

Hom.:

4427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0887

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.268

Gnomad EAS

AF:

0.00578

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.206

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

GnomAD4 genome

AF:

0.216

AC:

32831

AN:

152054

Hom.:

4428

Cov.:

AF XY:

0.210

AC XY:

15617

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.0885

AC:

3675

AN:

41534

American (AMR)

AF:

0.169

AC:

2572

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

931

AN:

3470

East Asian (EAS)

AF:

0.00579

AC:

AN:

5178

South Asian (SAS)

AF:

0.229

AC:

1100

AN:

4808

European-Finnish (FIN)

AF:

0.290

AC:

3067

AN:

10576

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20778

AN:

67906

Other (OTH)

AF:

0.203

AC:

429

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1214

2428

3642

4856

6070

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.273

Hom.:

5493

Bravo

AF:

0.199

Asia WGS

AF:

0.0940

AC:

326

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.023

(source)

DANN

Benign

0.26

PhyloP100

-2.0

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