Genetic Variant ENSG00000268797:n.118-23338_118-23337insAA (chr19-40868653-C-CAA) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000601627.1(ENSG00000268797):n.118-23338_118-23337insAA 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 0.13 ( 1735 hom., cov: 0)

Consequence

ENSG00000268797
ENST00000601627.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.52

Publications

2 publications found

Variant links:

Genes affected

ENSG00000268797 (HGNC:):

ENSG00000268797 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 = 0.242 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
ENSG00000268797	ENST00000601627.1 link	n.118-23338_118-23337insAA		intron_variant	Intron 1 of 3	3		ENSP00000469533.1		M0QY20

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

18003

AN:

140928

Hom.:

1733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.0880

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0914

Gnomad EAS

AF:

0.0673

Gnomad SAS

AF:

0.0579

Gnomad FIN

AF:

0.0419

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.0764

Gnomad OTH

AF:

0.141

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

GnomAD4 genome

AF:

0.128

AC:

18023

AN:

140980

Hom.:

1735

Cov.:

AF XY:

0.124

AC XY:

8445

AN XY:

68048

show subpopulations

African (AFR)

AF:

0.247

AC:

9537

AN:

38680

American (AMR)

AF:

0.139

AC:

1955

AN:

14060

Ashkenazi Jewish (ASJ)

AF:

0.0914

AC:

304

AN:

3326

East Asian (EAS)

AF:

0.0678

AC:

306

AN:

4516

South Asian (SAS)

AF:

0.0574

AC:

249

AN:

4338

European-Finnish (FIN)

AF:

0.0419

AC:

352

AN:

8392

Middle Eastern (MID)

AF:

0.157

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.0763

AC:

4930

AN:

64576

Other (OTH)

AF:

0.140

AC:

268

AN:

1920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

656

1313

1969

2626

3282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0541

Hom.:

1219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-3.5

Splicing

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

Publications

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19-40868653-CAA-CAAAA

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