dbSNP rs11398689: ENSG00000285163:n.393+1339_393+1340insG (chr16-85933613-T-TG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000645383.1(ENSG00000285163):n.393+1339_393+1340insG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 38608 hom., cov: 0)

Consequence

ENSG00000285163
ENST00000645383.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.902

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285163 (HGNC:):

ENSG00000285163 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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
ENSG00000285163	ENST00000645383.1 link	n.393+1339_393+1340insG		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1 link	n.77+8553_77+8554insG		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.719

AC:

104792

AN:

145810

Hom.:

38557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.895

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.567

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.724

Gnomad MID

AF:

0.517

Gnomad NFE

AF:

0.629

Gnomad OTH

AF:

0.657

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

GnomAD4 genome

AF:

0.719

AC:

104890

AN:

145890

Hom.:

38608

Cov.:

AF XY:

0.721

AC XY:

50754

AN XY:

70346

show subpopulations

African (AFR)

AF:

0.895

AC:

35290

AN:

39410

American (AMR)

AF:

0.704

AC:

10400

AN:

14778

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

1951

AN:

3438

East Asian (EAS)

AF:

0.761

AC:

3786

AN:

4978

South Asian (SAS)

AF:

0.667

AC:

3076

AN:

4614

European-Finnish (FIN)

AF:

0.724

AC:

6217

AN:

8584

Middle Eastern (MID)

AF:

0.525

AC:

146

AN:

278

European-Non Finnish (NFE)

AF:

0.629

AC:

42083

AN:

66894

Other (OTH)

AF:

0.659

AC:

1330

AN:

2018

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1339

2678

4018

5357

6696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.482

Hom.:

1077

Asia WGS

AF:

0.721

AC:

2496

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.90

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