Genetic Variant ENSG00000299769:n.282+6399T>C (chr6-32420769-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000766247.1(ENSG00000299769):n.282+6399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,186 control chromosomes in the GnomAD database, including 49,537 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 0.80 ( 49537 hom., cov: 32)

Consequence

ENSG00000299769
ENST00000766247.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

9 publications found

Variant links:

Genes affected

ENSG00000299769 (HGNC:):

ENSG00000299769 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299769	ENST00000766247.1 link	n.282+6399T>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1 link	n.287-4599T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.805

AC:

122364

AN:

152068

Hom.:

49505

Cov.:

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.863

Gnomad AMR

AF:

0.817

Gnomad ASJ

AF:

0.899

Gnomad EAS

AF:

0.976

Gnomad SAS

AF:

0.928

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.787

Gnomad OTH

AF:

0.809

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

GnomAD4 genome

AF:

0.805

AC:

122448

AN:

152186

Hom.:

49537

Cov.:

AF XY:

0.810

AC XY:

60282

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.769

AC:

31903

AN:

41506

American (AMR)

AF:

0.817

AC:

12487

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.899

AC:

3122

AN:

3472

East Asian (EAS)

AF:

0.976

AC:

5062

AN:

5186

South Asian (SAS)

AF:

0.928

AC:

4480

AN:

4830

European-Finnish (FIN)

AF:

0.859

AC:

9094

AN:

10588

Middle Eastern (MID)

AF:

0.874

AC:

257

AN:

294

European-Non Finnish (NFE)

AF:

0.787

AC:

53544

AN:

68006

Other (OTH)

AF:

0.812

AC:

1712

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1227

2454

3681

4908

6135

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

876

1752

2628

3504

4380

<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:

0.794

Hom.:

16099

Bravo

AF:

0.797

Asia WGS

AF:

0.922

AC:

3204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.11

(source)

DANN

Benign

0.76

PhyloP100

-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over