Genetic Variant ENSG00000306648:n.348+15614_348+15615insTA (chr3-191728221-C-CTA) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000819945.1(ENSG00000306648):n.348+15614_348+15615insTA 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 0.30 ( 7125 hom., cov: 0)

Consequence

ENSG00000306648
ENST00000819945.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.335

Publications

3 publications found

Variant links:

Genes affected

ENSG00000306648 (HGNC:):

ENSG00000306648 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 (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819945.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306648	ENST00000819945.1		n.348+15614_348+15615insTA		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.300

AC:

45498

AN:

151656

Hom.:

7114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.281

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

GnomAD4 genome

AF:

0.300

AC:

45527

AN:

151774

Hom.:

7125

Cov.:

AF XY:

0.306

AC XY:

22725

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.202

AC:

8353

AN:

41426

American (AMR)

AF:

0.276

AC:

4210

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1213

AN:

3462

East Asian (EAS)

AF:

0.411

AC:

2113

AN:

5144

South Asian (SAS)

AF:

0.394

AC:

1897

AN:

4812

European-Finnish (FIN)

AF:

0.398

AC:

4181

AN:

10500

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.331

AC:

22504

AN:

67892

Other (OTH)

AF:

0.284

AC:

598

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1581

3162

4742

6323

7904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.315

Hom.:

797

Asia WGS

AF:

0.411

AC:

1423

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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3-191728221-CTA-CTATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over