Genetic Variant ENSG00000229066:n.247+67091G>C (chr2-175324679-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 ENST00000438963.2(ENSG00000229066):n.247+67091G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,198 control chromosomes in the GnomAD database, including 2,686 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 0.18 ( 2686 hom., cov: 32)

Consequence

ENSG00000229066
ENST00000438963.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

Publications

3 publications found

Variant links:

Genes affected

ENSG00000229066 (HGNC:):

ENSG00000229066 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000229066	ENST00000438963.2 link	n.247+67091G>C	intron_variant	Intron 1 of 2	3
ENSG00000229066	ENST00000444567.1 link	n.448+33178G>C	intron_variant	Intron 2 of 2	3
ENSG00000229066	ENST00000653625.1 link	n.336+33178G>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27851

AN:

152080

Hom.:

2671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.210

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

GnomAD4 genome

AF:

0.183

AC:

27906

AN:

152198

Hom.:

2686

Cov.:

AF XY:

0.186

AC XY:

13838

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.145

AC:

6040

AN:

41524

American (AMR)

AF:

0.229

AC:

3502

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

738

AN:

3462

East Asian (EAS)

AF:

0.377

AC:

1952

AN:

5180

South Asian (SAS)

AF:

0.211

AC:

1019

AN:

4824

European-Finnish (FIN)

AF:

0.167

AC:

1768

AN:

10592

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.179

AC:

12165

AN:

68004

Other (OTH)

AF:

0.212

AC:

449

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1202

2405

3607

4810

6012

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<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:

0.0770

Hom.:

Bravo

AF:

0.188

Asia WGS

AF:

0.296

AC:

1029

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.9

(source)

DANN

Benign

0.44

PhyloP100

0.14

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.99

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