Genetic Variant ENSG00000300599:n.458+33091C>T (chr20-39252839-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000772859.1(ENSG00000300599):n.458+33091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,084 control chromosomes in the GnomAD database, including 12,989 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 0.40 ( 12989 hom., cov: 33)

Consequence

ENSG00000300599
ENST00000772859.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.235

Publications

11 publications found

Variant links:

Genes affected

ENSG00000300599 (HGNC:):

ENSG00000300599 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300599	ENST00000772859.1 link	n.458+33091C>T	intron_variant	Intron 2 of 2
ENSG00000300599	ENST00000772860.1 link	n.314-31177C>T	intron_variant	Intron 3 of 3
ENSG00000300599	ENST00000772861.1 link	n.314-28887C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61493

AN:

151966

Hom.:

12963

Cov.:

show subpopulations

Gnomad AFR

AF:

0.479

Gnomad AMI

AF:

0.447

Gnomad AMR

AF:

0.483

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.367

Gnomad OTH

AF:

0.404

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

GnomAD4 genome

AF:

0.405

AC:

61588

AN:

152084

Hom.:

12989

Cov.:

AF XY:

0.405

AC XY:

30154

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.480

AC:

19910

AN:

41472

American (AMR)

AF:

0.483

AC:

7384

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1405

AN:

3468

East Asian (EAS)

AF:

0.187

AC:

967

AN:

5168

South Asian (SAS)

AF:

0.358

AC:

1726

AN:

4818

European-Finnish (FIN)

AF:

0.367

AC:

3886

AN:

10586

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.367

AC:

24932

AN:

67968

Other (OTH)

AF:

0.404

AC:

852

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1857

3714

5572

7429

9286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.376

Hom.:

47234

Bravo

AF:

0.418

Asia WGS

AF:

0.362

AC:

1256

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.1

(source)

DANN

Benign

0.58

PhyloP100

-0.23

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