Genetic Variant ENSG00000299747:n.279+559C>G (chr6-32437585-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000766007.1(ENSG00000299747):n.279+559C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,028 control chromosomes in the GnomAD database, including 30,308 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 0.63 ( 30308 hom., cov: 31)

Consequence

ENSG00000299747
ENST00000766007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.255

Publications

30 publications found

Variant links:

Genes affected

ENSG00000299747 (HGNC:):

ENSG00000299747 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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
ENSG00000299747	ENST00000766007.1 link	n.279+559C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.626

AC:

95054

AN:

151910

Hom.:

30305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.676

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.705

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.646

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

GnomAD4 genome

AF:

0.626

AC:

95098

AN:

152028

Hom.:

30308

Cov.:

AF XY:

0.631

AC XY:

46868

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.487

AC:

20175

AN:

41436

American (AMR)

AF:

0.659

AC:

10075

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

2316

AN:

3472

East Asian (EAS)

AF:

0.715

AC:

3691

AN:

5164

South Asian (SAS)

AF:

0.698

AC:

3367

AN:

4826

European-Finnish (FIN)

AF:

0.705

AC:

7458

AN:

10578

Middle Eastern (MID)

AF:

0.724

AC:

213

AN:

294

European-Non Finnish (NFE)

AF:

0.674

AC:

45827

AN:

67964

Other (OTH)

AF:

0.647

AC:

1361

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1787

3575

5362

7150

8937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.666

Hom.:

18804

Bravo

AF:

0.615

Asia WGS

AF:

0.676

AC:

2353

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

9.0

(source)

DANN

Benign

0.75

PhyloP100

-0.26

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