Genetic Variant :null (chr11-636784-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 0.427 in 147,208 control chromosomes in the GnomAD database, including 13,621 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 0.43 ( 13621 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.559

Publications

231 publications found

Variant links:

COSMIC-nc: COSV51563474

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ACMG classification

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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:

0.427

AC:

62856

AN:

147106

Hom.:

13615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.391

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.428

Gnomad FIN

AF:

0.425

Gnomad MID

AF:

0.452

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.461

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

GnomAD4 genome

AF:

0.427

AC:

62895

AN:

147208

Hom.:

13621

Cov.:

AF XY:

0.426

AC XY:

30532

AN XY:

71648

show subpopulations

African (AFR)

AF:

0.400

AC:

15816

AN:

39538

American (AMR)

AF:

0.390

AC:

5781

AN:

14834

Ashkenazi Jewish (ASJ)

AF:

0.546

AC:

1874

AN:

3432

East Asian (EAS)

AF:

0.384

AC:

1854

AN:

4830

South Asian (SAS)

AF:

0.427

AC:

1969

AN:

4616

European-Finnish (FIN)

AF:

0.425

AC:

4188

AN:

9862

Middle Eastern (MID)

AF:

0.469

AC:

135

AN:

288

European-Non Finnish (NFE)

AF:

0.450

AC:

30088

AN:

66906

Other (OTH)

AF:

0.461

AC:

935

AN:

2028

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

1620

3240

4860

6480

8100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<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:

0.437

Hom.:

3785

Bravo

AF:

0.423

Asia WGS

AF:

0.403

AC:

1400

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.69

(source)

DANN

Benign

0.41

PhyloP100

-0.56

PromoterAI

0.012

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