Genetic Variant :null (chr1-115192428-C-T) – 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 0.258 in 152,108 control chromosomes in the GnomAD database, including 6,453 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 0.26 ( 6453 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

3 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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:

0.258

AC:

39287

AN:

151990

Hom.:

6454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0876

Gnomad AMI

AF:

0.300

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.00309

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.292

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

GnomAD4 genome

AF:

0.258

AC:

39270

AN:

152108

Hom.:

6453

Cov.:

AF XY:

0.251

AC XY:

18684

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0874

AC:

3628

AN:

41526

American (AMR)

AF:

0.226

AC:

3457

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.425

AC:

1474

AN:

3472

East Asian (EAS)

AF:

0.00310

AC:

AN:

5160

South Asian (SAS)

AF:

0.166

AC:

800

AN:

4822

European-Finnish (FIN)

AF:

0.350

AC:

3689

AN:

10554

Middle Eastern (MID)

AF:

0.366

AC:

107

AN:

292

European-Non Finnish (NFE)

AF:

0.371

AC:

25214

AN:

67978

Other (OTH)

AF:

0.290

AC:

612

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1352

2704

4056

5408

6760

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.302

Hom.:

1355

Bravo

AF:

0.244

Asia WGS

AF:

0.0880

AC:

309

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.086

(source)

DANN

Benign

0.58

PhyloP100

-2.2

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