Genetic Variant :null (chr4-110748064-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 0.694 in 151,566 control chromosomes in the GnomAD database, including 37,944 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 0.69 ( 37944 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.434

Publications

15 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 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:

0.694

AC:

105074

AN:

151448

Hom.:

37927

Cov.:

show subpopulations

Gnomad AFR

AF:

0.583

Gnomad AMI

AF:

0.928

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.630

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.803

Gnomad OTH

AF:

0.702

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

GnomAD4 genome

AF:

0.694

AC:

105120

AN:

151566

Hom.:

37944

Cov.:

AF XY:

0.683

AC XY:

50573

AN XY:

74098

show subpopulations

African (AFR)

AF:

0.583

AC:

24099

AN:

41354

American (AMR)

AF:

0.594

AC:

9012

AN:

15174

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2126

AN:

3454

East Asian (EAS)

AF:

0.262

AC:

1347

AN:

5140

South Asian (SAS)

AF:

0.631

AC:

3028

AN:

4802

European-Finnish (FIN)

AF:

0.809

AC:

8566

AN:

10586

Middle Eastern (MID)

AF:

0.687

AC:

202

AN:

294

European-Non Finnish (NFE)

AF:

0.803

AC:

54422

AN:

67750

Other (OTH)

AF:

0.701

AC:

1472

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1515

3031

4546

6062

7577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<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:

0.670

Hom.:

10925

Bravo

AF:

0.673

Asia WGS

AF:

0.468

AC:

1630

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.65

(source)

DANN

Benign

0.48

PhyloP100

-0.43

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