Genetic Variant :null (chr6-43769749-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 0.559 in 151,884 control chromosomes in the GnomAD database, including 24,103 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 0.56 ( 24103 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.265

Publications

555 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=-0.6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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:

0.559

AC:

84807

AN:

151766

Hom.:

24081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.659

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.725

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.582

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

GnomAD4 genome

AF:

0.559

AC:

84887

AN:

151884

Hom.:

24103

Cov.:

AF XY:

0.557

AC XY:

41324

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.659

AC:

27325

AN:

41450

American (AMR)

AF:

0.590

AC:

9007

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.535

AC:

1858

AN:

3472

East Asian (EAS)

AF:

0.726

AC:

3722

AN:

5130

South Asian (SAS)

AF:

0.552

AC:

2654

AN:

4806

European-Finnish (FIN)

AF:

0.448

AC:

4713

AN:

10524

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.500

AC:

33973

AN:

67920

Other (OTH)

AF:

0.583

AC:

1231

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1872

3744

5615

7487

9359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.532

Hom.:

38625

Bravo

AF:

0.578

Asia WGS

AF:

0.606

AC:

2104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

-0.27

PromoterAI

-0.022

Neutral

(source)

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