Genetic Variant :null (chr14-85011409-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 0.399 in 151,940 control chromosomes in the GnomAD database, including 13,329 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 0.40 ( 13329 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.359

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=-0.88).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.545 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:

0.399

AC:

60578

AN:

151820

Hom.:

13318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.543

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.465

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.435

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

GnomAD4 genome

AF:

0.399

AC:

60607

AN:

151940

Hom.:

13329

Cov.:

AF XY:

0.399

AC XY:

29618

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.224

AC:

9270

AN:

41444

American (AMR)

AF:

0.555

AC:

8473

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.543

AC:

1885

AN:

3470

East Asian (EAS)

AF:

0.293

AC:

1509

AN:

5158

South Asian (SAS)

AF:

0.466

AC:

2240

AN:

4804

European-Finnish (FIN)

AF:

0.354

AC:

3733

AN:

10548

Middle Eastern (MID)

AF:

0.476

AC:

140

AN:

294

European-Non Finnish (NFE)

AF:

0.471

AC:

32000

AN:

67938

Other (OTH)

AF:

0.429

AC:

906

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1740

3479

5219

6958

8698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.465

Hom.:

21253

Bravo

AF:

0.407

Asia WGS

AF:

0.345

AC:

1191

AN:

3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

(source)

DANN

Benign

0.74

PhyloP100

-0.36

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