Genetic Variant ENSG00000268797:n.118-23338_118-23337insA (chr19-40868653-C-CA) – 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_118-23337insA 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 0.67 ( 31706 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 (EAS) allele frequency at 95% confidence interval = 0.691 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_118-23337insA		intron_variant	Intron 1 of 3	3		ENSP00000469533.1		M0QY20

Frequencies

GnomAD3 genomes

AF:

0.668

AC:

94238

AN:

141022

Hom.:

31697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.637

Gnomad AMR

AF:

0.642

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.712

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.578

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.629

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

GnomAD4 genome

AF:

0.668

AC:

94266

AN:

141078

Hom.:

31706

Cov.:

AF XY:

0.671

AC XY:

45717

AN XY:

68102

show subpopulations

African (AFR)

AF:

0.653

AC:

25276

AN:

38706

American (AMR)

AF:

0.642

AC:

9040

AN:

14082

Ashkenazi Jewish (ASJ)

AF:

0.691

AC:

2301

AN:

3330

East Asian (EAS)

AF:

0.712

AC:

3209

AN:

4510

South Asian (SAS)

AF:

0.584

AC:

2531

AN:

4334

European-Finnish (FIN)

AF:

0.778

AC:

6556

AN:

8430

Middle Eastern (MID)

AF:

0.569

AC:

156

AN:

274

European-Non Finnish (NFE)

AF:

0.672

AC:

43411

AN:

64586

Other (OTH)

AF:

0.630

AC:

1215

AN:

1930

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1407

2813

4220

5626

7033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.626

Hom.:

1219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-3.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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chr19-40868653-C-CA

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