Genetic Variant :null (chr5-151096443-T-C) – 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 0.189 in 152,098 control chromosomes in the GnomAD database, including 3,444 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 0.19 ( 3444 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

9 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 (EAS) allele frequency at 95% confidence interval = 0.347 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:

0.189

AC:

28662

AN:

151980

Hom.:

3424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.293

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.190

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

GnomAD4 genome

AF:

0.189

AC:

28721

AN:

152098

Hom.:

3444

Cov.:

AF XY:

0.192

AC XY:

14297

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.325

AC:

13452

AN:

41422

American (AMR)

AF:

0.118

AC:

1798

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

488

AN:

3472

East Asian (EAS)

AF:

0.361

AC:

1866

AN:

5176

South Asian (SAS)

AF:

0.292

AC:

1406

AN:

4822

European-Finnish (FIN)

AF:

0.140

AC:

1478

AN:

10590

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7692

AN:

68012

Other (OTH)

AF:

0.199

AC:

419

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1116

2232

3347

4463

5579

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.133

Hom.:

2877

Bravo

AF:

0.190

Asia WGS

AF:

0.403

AC:

1396

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.5

(source)

DANN

Benign

0.68

PhyloP100

0.036

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