Genetic Variant :null (chr6-31574705-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 0.088 in 151,940 control chromosomes in the GnomAD database, including 838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.088 ( 838 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

risk factor no assertion criteria provided O:2

Conservation

PhyloP100: -1.39

Publications

702 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.167 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:

0.0879

AC:

13352

AN:

151822

Hom.:

835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0309

Gnomad AMI

AF:

0.0826

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0557

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.0939

Gnomad OTH

AF:

0.0986

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

GnomAD4 genome

AF:

0.0880

AC:

13375

AN:

151940

Hom.:

838

Cov.:

AF XY:

0.0898

AC XY:

6666

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.0309

AC:

1280

AN:

41444

American (AMR)

AF:

0.172

AC:

2632

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

887

AN:

3472

East Asian (EAS)

AF:

0.132

AC:

679

AN:

5136

South Asian (SAS)

AF:

0.123

AC:

589

AN:

4806

European-Finnish (FIN)

AF:

0.0557

AC:

588

AN:

10566

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0940

AC:

6383

AN:

67936

Other (OTH)

AF:

0.103

AC:

218

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

588

1176

1765

2353

2941

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.104

Hom.:

3298

Bravo

AF:

0.0935

Asia WGS

AF:

0.116

AC:

404

AN:

3478

ClinVar

ClinVar submissions

Significance:risk factor

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

ALZHEIMER DISEASE, SUSCEPTIBILITY TO (1)

VASCULAR DEMENTIA, SUSCEPTIBILITY TO (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.5

(source)

DANN

Benign

0.46

PhyloP100

-1.4

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