dbSNP rs444984: :null (chr5-155067396-C-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 0.42 in 152,010 control chromosomes in the GnomAD database, including 15,063 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 ( 15063 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

5 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=-0.57).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 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:

0.420

AC:

63778

AN:

151890

Hom.:

15062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.496

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.435

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

GnomAD4 genome

AF:

0.420

AC:

63786

AN:

152010

Hom.:

15063

Cov.:

AF XY:

0.422

AC XY:

31326

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.205

AC:

8494

AN:

41458

American (AMR)

AF:

0.432

AC:

6607

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.479

AC:

1660

AN:

3468

East Asian (EAS)

AF:

0.214

AC:

1104

AN:

5166

South Asian (SAS)

AF:

0.520

AC:

2501

AN:

4814

European-Finnish (FIN)

AF:

0.496

AC:

5239

AN:

10554

Middle Eastern (MID)

AF:

0.493

AC:

144

AN:

292

European-Non Finnish (NFE)

AF:

0.538

AC:

36576

AN:

67952

Other (OTH)

AF:

0.433

AC:

912

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1775

3550

5325

7100

8875

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<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:

0.491

Hom.:

52536

Bravo

AF:

0.399

Asia WGS

AF:

0.357

AC:

1243

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

(source)

DANN

Benign

0.92

PhyloP100

-0.37

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