Genetic Variant ENSG00000233359:n.339+16818A>G (chr1-102370387-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 ENST00000447916.1(ENSG00000233359):n.339+16818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,034 control chromosomes in the GnomAD database, including 55,951 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 0.84 ( 55951 hom., cov: 31)

Consequence

ENSG00000233359
ENST00000447916.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215

Publications

1 publications found

Variant links:

Genes affected

ENSG00000233359 (HGNC:58374):

ENSG00000233359 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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
ENSG00000233359	ENST00000447916.1 link	n.339+16818A>G		intron_variant	Intron 4 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.843

AC:

128056

AN:

151916

Hom.:

55936

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.995

Gnomad AMR

AF:

0.904

Gnomad ASJ

AF:

0.946

Gnomad EAS

AF:

0.977

Gnomad SAS

AF:

0.907

Gnomad FIN

AF:

0.970

Gnomad MID

AF:

0.921

Gnomad NFE

AF:

0.942

Gnomad OTH

AF:

0.867

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

GnomAD4 genome

AF:

0.843

AC:

128113

AN:

152034

Hom.:

55951

Cov.:

AF XY:

0.847

AC XY:

62977

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.586

AC:

24260

AN:

41410

American (AMR)

AF:

0.904

AC:

13812

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.946

AC:

3284

AN:

3470

East Asian (EAS)

AF:

0.977

AC:

5055

AN:

5176

South Asian (SAS)

AF:

0.908

AC:

4384

AN:

4826

European-Finnish (FIN)

AF:

0.970

AC:

10253

AN:

10570

Middle Eastern (MID)

AF:

0.915

AC:

269

AN:

294

European-Non Finnish (NFE)

AF:

0.942

AC:

64056

AN:

67992

Other (OTH)

AF:

0.868

AC:

1833

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

831

1662

2493

3324

4155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<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:

0.867

Hom.:

7229

Bravo

AF:

0.824

Asia WGS

AF:

0.908

AC:

3144

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.9

(source)

DANN

Benign

0.55

PhyloP100

-0.21

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