Genetic Variant ENST00000806334.1:n.281-9199G>A (chr20-48300766-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000806334.1(ENSG00000304799):n.281-9199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 151,620 control chromosomes in the GnomAD database, including 594 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 0.060 ( 594 hom., cov: 32)

Consequence

ENSG00000304799
ENST00000806334.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.334

Publications

0 publications found

Variant links:

Genes affected

ENSG00000304799 (HGNC:):

ENSG00000304799 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 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
ENSG00000304799	ENST00000806334.1 link	n.281-9199G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0597

AC:

9049

AN:

151502

Hom.:

588

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0610

Gnomad ASJ

AF:

0.00636

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.0681

Gnomad FIN

AF:

0.0174

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00930

Gnomad OTH

AF:

0.0563

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

GnomAD4 genome

AF:

0.0599

AC:

9081

AN:

151620

Hom.:

594

Cov.:

AF XY:

0.0614

AC XY:

4549

AN XY:

74078

show subpopulations

African (AFR)

AF:

0.137

AC:

5653

AN:

41286

American (AMR)

AF:

0.0612

AC:

929

AN:

15192

Ashkenazi Jewish (ASJ)

AF:

0.00636

AC:

AN:

3460

East Asian (EAS)

AF:

0.235

AC:

1208

AN:

5138

South Asian (SAS)

AF:

0.0684

AC:

325

AN:

4752

European-Finnish (FIN)

AF:

0.0174

AC:

184

AN:

10554

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00930

AC:

632

AN:

67936

Other (OTH)

AF:

0.0571

AC:

120

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

401

802

1204

1605

2006

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0353

Hom.:

Bravo

AF:

0.0670

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

0.33

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