Genetic Variant ENST00000645383.1:n.393+1284_393+1285insATG (chr16-85933558-C-CATG) – 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+1284_393+1285insATG 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 0.46 ( 14514 hom., cov: 0)

Consequence

ENSG00000285163
ENST00000645383.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.890

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285163 (HGNC:):

ENSG00000285163 links:

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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 = 0.588 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+1284_393+1285insATG		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1 link	n.77+8498_77+8499insATG		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.456

AC:

62980

AN:

138088

Hom.:

14485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.594

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.395

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.516

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.470

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.433

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

GnomAD4 genome

AF:

0.456

AC:

63050

AN:

138162

Hom.:

14514

Cov.:

AF XY:

0.460

AC XY:

30440

AN XY:

66184

show subpopulations

African (AFR)

AF:

0.595

AC:

22102

AN:

37172

American (AMR)

AF:

0.395

AC:

5304

AN:

13432

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1454

AN:

3388

East Asian (EAS)

AF:

0.515

AC:

2435

AN:

4726

South Asian (SAS)

AF:

0.425

AC:

1812

AN:

4264

European-Finnish (FIN)

AF:

0.447

AC:

3456

AN:

7732

Middle Eastern (MID)

AF:

0.483

AC:

117

AN:

242

European-Non Finnish (NFE)

AF:

0.390

AC:

25149

AN:

64470

Other (OTH)

AF:

0.434

AC:

809

AN:

1864

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1601

3202

4803

6404

8005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.388

Hom.:

1096

Asia WGS

AF:

0.441

AC:

1528

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.89

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