dbSNP rs4464522: :null (chr4-31239120-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 0.417 in 151,864 control chromosomes in the GnomAD database, including 14,463 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 0.42 ( 14463 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.634

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 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:

0.417

AC:

63332

AN:

151746

Hom.:

14431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.606

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.288

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.296

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.437

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

GnomAD4 genome

AF:

0.417

AC:

63402

AN:

151864

Hom.:

14463

Cov.:

AF XY:

0.416

AC XY:

30848

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.606

AC:

25087

AN:

41394

American (AMR)

AF:

0.331

AC:

5055

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1784

AN:

3470

East Asian (EAS)

AF:

0.287

AC:

1475

AN:

5134

South Asian (SAS)

AF:

0.446

AC:

2136

AN:

4792

European-Finnish (FIN)

AF:

0.296

AC:

3125

AN:

10568

Middle Eastern (MID)

AF:

0.578

AC:

170

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23328

AN:

67930

Other (OTH)

AF:

0.439

AC:

926

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1810

3619

5429

7238

9048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.382

Hom.:

1996

Bravo

AF:

0.428

Asia WGS

AF:

0.389

AC:

1355

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.35

PhyloP100

-0.63

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