Genetic Variant ENSG00000302363:n.323+428T>C (chr3-3186060-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 ENST00000786145.1(ENSG00000302363):n.323+428T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.922 in 152,188 control chromosomes in the GnomAD database, including 65,835 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 0.92 ( 65835 hom., cov: 31)

Consequence

ENSG00000302363
ENST00000786145.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.423

Publications

0 publications found

Variant links:

Genes affected

ENSG00000302363 (HGNC:):

ENSG00000302363 links:

Genome browser will be placed here

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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
ENSG00000302363	ENST00000786145.1 link	n.323+428T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.922

AC:

140279

AN:

152070

Hom.:

65790

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.966

Gnomad ASJ

AF:

0.999

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.965

Gnomad NFE

AF:

0.998

Gnomad OTH

AF:

0.944

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

GnomAD4 genome

AF:

0.922

AC:

140384

AN:

152188

Hom.:

65835

Cov.:

AF XY:

0.925

AC XY:

68870

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.734

AC:

30421

AN:

41444

American (AMR)

AF:

0.966

AC:

14761

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.999

AC:

3469

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5176

AN:

5176

South Asian (SAS)

AF:

0.999

AC:

4822

AN:

4826

European-Finnish (FIN)

AF:

1.00

AC:

10625

AN:

10626

Middle Eastern (MID)

AF:

0.973

AC:

286

AN:

294

European-Non Finnish (NFE)

AF:

0.998

AC:

67915

AN:

68038

Other (OTH)

AF:

0.945

AC:

1997

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

445

890

1334

1779

2224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

900

1800

2700

3600

4500

<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:

0.956

Hom.:

8347

Bravo

AF:

0.910

Asia WGS

AF:

0.983

AC:

3420

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

4.7

(source)

DANN

Benign

0.65

PhyloP100

0.42

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