Genetic Variant :null (chr6-170281387-G-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 0.466 in 152,100 control chromosomes in the GnomAD database, including 17,688 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 0.47 ( 17688 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

13 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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:

0.466

AC:

70878

AN:

151982

Hom.:

17666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.992

Gnomad SAS

AF:

0.598

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.480

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

GnomAD4 genome

AF:

0.466

AC:

70939

AN:

152100

Hom.:

17688

Cov.:

AF XY:

0.472

AC XY:

35107

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.342

AC:

14181

AN:

41484

American (AMR)

AF:

0.492

AC:

7518

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

1748

AN:

3470

East Asian (EAS)

AF:

0.992

AC:

5133

AN:

5176

South Asian (SAS)

AF:

0.596

AC:

2875

AN:

4820

European-Finnish (FIN)

AF:

0.528

AC:

5583

AN:

10574

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32391

AN:

67978

Other (OTH)

AF:

0.485

AC:

1022

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1880

3760

5639

7519

9399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<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:

0.464

Hom.:

10533

Bravo

AF:

0.461

Asia WGS

AF:

0.787

AC:

2734

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.083

(source)

DANN

Benign

0.60

PhyloP100

-1.5

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