Genetic Variant :null (chr18-60183864-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 0.237 in 152,140 control chromosomes in the GnomAD database, including 4,475 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 0.24 ( 4475 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.757

Publications

637 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 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:

0.237

AC:

36072

AN:

152022

Hom.:

4474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.158

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.183

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.237

AC:

36110

AN:

152140

Hom.:

4475

Cov.:

AF XY:

0.234

AC XY:

17380

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.283

AC:

11745

AN:

41492

American (AMR)

AF:

0.158

AC:

2417

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.200

AC:

696

AN:

3472

East Asian (EAS)

AF:

0.183

AC:

949

AN:

5178

South Asian (SAS)

AF:

0.351

AC:

1689

AN:

4816

European-Finnish (FIN)

AF:

0.171

AC:

1809

AN:

10590

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15967

AN:

67990

Other (OTH)

AF:

0.223

AC:

471

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1408

2816

4225

5633

7041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.234

Hom.:

17366

Bravo

AF:

0.236

Asia WGS

AF:

0.226

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.2

(source)

DANN

Benign

0.73

PhyloP100

0.76

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