Genetic Variant ENST00000829268.1:n.360-28834A>G (chr13-59245009-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 ENST00000829268.1(ENSG00000307835):n.360-28834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,094 control chromosomes in the GnomAD database, including 5,027 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 0.24 ( 5027 hom., cov: 32)

Consequence

ENSG00000307835
ENST00000829268.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180

Publications

1 publications found

Variant links:

Genes affected

ENSG00000307835 (HGNC:):

ENSG00000307835 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000307835	ENST00000829268.1 link	n.360-28834A>G	intron_variant	Intron 2 of 2
ENSG00000307835	ENST00000829269.1 link	n.558+27222A>G	intron_variant	Intron 4 of 4
ENSG00000307835	ENST00000829270.1 link	n.263+27222A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36148

AN:

151976

Hom.:

5028

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.555

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.128

Gnomad EAS

AF:

0.0112

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.210

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

GnomAD4 genome

AF:

0.238

AC:

36153

AN:

152094

Hom.:

5027

Cov.:

AF XY:

0.236

AC XY:

17537

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.138

AC:

5724

AN:

41490

American (AMR)

AF:

0.191

AC:

2913

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

444

AN:

3472

East Asian (EAS)

AF:

0.0110

AC:

AN:

5178

South Asian (SAS)

AF:

0.228

AC:

1102

AN:

4824

European-Finnish (FIN)

AF:

0.319

AC:

3369

AN:

10556

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21529

AN:

67982

Other (OTH)

AF:

0.208

AC:

439

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1366

2731

4097

5462

6828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

380

760

1140

1520

1900

<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:

0.161

Hom.:

371

Bravo

AF:

0.222

Asia WGS

AF:

0.118

AC:

410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.1

(source)

DANN

Benign

0.75

PhyloP100

0.18

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