Genetic Variant ENSG00000289326:n.852-8479G>C (chr2-27744393-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000813446.1(ENSG00000289326):n.852-8479G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,004 control chromosomes in the GnomAD database, including 2,202 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 ( 2202 hom., cov: 31)

Consequence

ENSG00000289326
ENST00000813446.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.470

Publications

10 publications found

Variant links:

Genes affected

ENSG00000289326 (HGNC:):

ENSG00000289326 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289326	ENST00000813446.1 link	n.852-8479G>C	intron_variant	Intron 3 of 4
ENSG00000289326	ENST00000813447.1 link	n.1064-8479G>C	intron_variant	Intron 2 of 4
ENSG00000289326	ENST00000813448.1 link	n.1088-8479G>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22753

AN:

151886

Hom.:

2204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0332

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.189

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

GnomAD4 genome

AF:

0.150

AC:

22750

AN:

152004

Hom.:

2202

Cov.:

AF XY:

0.152

AC XY:

11270

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.0331

AC:

1375

AN:

41502

American (AMR)

AF:

0.165

AC:

2516

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

846

AN:

3464

East Asian (EAS)

AF:

0.338

AC:

1745

AN:

5162

South Asian (SAS)

AF:

0.163

AC:

783

AN:

4810

European-Finnish (FIN)

AF:

0.193

AC:

2034

AN:

10534

Middle Eastern (MID)

AF:

0.267

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.189

AC:

12870

AN:

67966

Other (OTH)

AF:

0.191

AC:

403

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

946

1892

2838

3784

4730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.0869

Hom.:

134

Bravo

AF:

0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.22

(source)

DANN

Benign

0.42

PhyloP100

-0.47

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