Genetic Variant :null (chr14-82363875-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 0.485 in 151,060 control chromosomes in the GnomAD database, including 18,434 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 0.48 ( 18434 hom., cov: 29)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

Publications

5 publications found

Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.628 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:

0.485

AC:

73192

AN:

150942

Hom.:

18440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.498

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

GnomAD4 genome

AF:

0.485

AC:

73205

AN:

151060

Hom.:

18434

Cov.:

AF XY:

0.489

AC XY:

36095

AN XY:

73768

show subpopulations

African (AFR)

AF:

0.375

AC:

15401

AN:

41094

American (AMR)

AF:

0.467

AC:

7059

AN:

15130

Ashkenazi Jewish (ASJ)

AF:

0.601

AC:

2087

AN:

3470

East Asian (EAS)

AF:

0.367

AC:

1877

AN:

5120

South Asian (SAS)

AF:

0.647

AC:

3078

AN:

4758

European-Finnish (FIN)

AF:

0.570

AC:

5959

AN:

10454

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.529

AC:

35863

AN:

67754

Other (OTH)

AF:

0.491

AC:

1021

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1808

3617

5425

7234

9042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.517

Hom.:

86504

Bravo

AF:

0.470

Asia WGS

AF:

0.463

AC:

1611

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

8.5

(source)

DANN

Benign

0.75

PhyloP100

-2.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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