Genetic Variant ENSG00000309058:n.329-1375A>G (chr8-12834362-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 ENST00000838107.1(ENSG00000309058):n.329-1375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,234 control chromosomes in the GnomAD database, including 1,922 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 0.15 ( 1922 hom., cov: 33)

Consequence

ENSG00000309058
ENST00000838107.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104

Publications

5 publications found

Variant links:

Genes affected

ENSG00000309058 (HGNC:):

ENSG00000309058 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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
ENSG00000309058	ENST00000838107.1 link	n.329-1375A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22621

AN:

152116

Hom.:

1914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.168

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

GnomAD4 genome

AF:

0.149

AC:

22649

AN:

152234

Hom.:

1922

Cov.:

AF XY:

0.150

AC XY:

11196

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.178

AC:

7381

AN:

41526

American (AMR)

AF:

0.225

AC:

3436

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

466

AN:

3470

East Asian (EAS)

AF:

0.260

AC:

1345

AN:

5182

South Asian (SAS)

AF:

0.200

AC:

962

AN:

4822

European-Finnish (FIN)

AF:

0.101

AC:

1070

AN:

10608

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7551

AN:

68008

Other (OTH)

AF:

0.169

AC:

356

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

961

1923

2884

3846

4807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.156

Hom.:

1293

Bravo

AF:

0.160

Asia WGS

AF:

0.248

AC:

860

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.3

(source)

DANN

Benign

0.33

PhyloP100

-0.10

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