dbSNP rs5830914: CRIPT:n.608+57_608+58insG (chr2-46617080-C-CG) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000486447.1(CRIPT):n.608+57_608+58insG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 1.0 ( 75831 hom., cov: 0)

Exomes 𝑓: 1.0 ( 275335 hom. )

Consequence

CRIPT
ENST00000486447.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0240

Publications

3 publications found

Variant links:

Genes affected

CRIPT (HGNC:14312): (CXXC repeat containing interactor of PDZ3 domain) This gene encodes a protein that binds to the PDZ3 peptide recognition domain. The encoded protein may modulates protein interactions with the cytoskeleton. A mutation in this gene resulted in short stature with microcephaly and distinctive facies. [provided by RefSeq, Jun 2014]

CRIPT links:

PIGF (HGNC:8962): (phosphatidylinositol glycan anchor biosynthesis class F) This gene encodes a protein involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor, a glycolipid containing three mannose molecules in its core backbone, is found on many blood cells where it serves to anchor proteins to the cell surface. The encoded protein and another GPI synthesis protein, PIGO, function in the transfer of ethanolaminephosphate to the third mannose in GPI. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

PIGF Gene-Disease associations (from GenCC):

onychodystrophy, osteodystrophy, impaired intellectual development, and seizures syndrome
Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

PIGF links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 2-46617080-C-CG is Benign according to our data. Variant chr2-46617080-C-CG is described in ClinVar as [Benign]. Clinvar id is 1240553.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIGF	NM_002643.4 link	c.-133_-132insC		upstream_gene_variant		ENST00000281382.11	NP_002634.1	Q07326-1Q6IB04
CRIPT	NM_014171.6 link	c.-203_-202insG		upstream_gene_variant		ENST00000238892.4	NP_054890.1	Q9P021

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGF	ENST00000281382.11 link	c.-133_-132insC		upstream_gene_variant		1	NM_002643.4	ENSP00000281382.6		Q07326-1
CRIPT	ENST00000238892.4 link	c.-203_-202insG		upstream_gene_variant		1	NM_014171.6	ENSP00000238892.3		Q9P021

Frequencies

GnomAD3 genomes

AF:

0.998

AC:

151878

AN:

152214

Hom.:

75772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.999

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.998

Gnomad ASJ

AF:

0.994

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

1.00

Gnomad FIN

AF:

0.994

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.997

Gnomad OTH

AF:

0.999

GnomAD4 exome

AF:

0.998

AC:

551895

AN:

553122

Hom.:

275335

Cov.:

AF XY:

0.998

AC XY:

292265

AN XY:

292910

show subpopulations

African (AFR)

AF:

0.999

AC:

15485

AN:

15498

American (AMR)

AF:

0.999

AC:

29261

AN:

29282

Ashkenazi Jewish (ASJ)

AF:

0.994

AC:

16468

AN:

16566

East Asian (EAS)

AF:

1.00

AC:

31655

AN:

31656

South Asian (SAS)

AF:

1.00

AC:

54578

AN:

54580

European-Finnish (FIN)

AF:

0.993

AC:

32009

AN:

32236

Middle Eastern (MID)

AF:

0.999

AC:

2302

AN:

2304

European-Non Finnish (NFE)

AF:

0.998

AC:

340156

AN:

340960

Other (OTH)

AF:

0.998

AC:

29981

AN:

30040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

120

179

239

299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.998

AC:

151996

AN:

152332

Hom.:

75831

Cov.:

AF XY:

0.998

AC XY:

74308

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.999

AC:

41554

AN:

41586

American (AMR)

AF:

0.998

AC:

15279

AN:

15314

Ashkenazi Jewish (ASJ)

AF:

0.994

AC:

3450

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5156

AN:

5156

South Asian (SAS)

AF:

1.00

AC:

4828

AN:

4828

European-Finnish (FIN)

AF:

0.994

AC:

10566

AN:

10626

Middle Eastern (MID)

AF:

1.00

AC:

294

AN:

294

European-Non Finnish (NFE)

AF:

0.997

AC:

67848

AN:

68032

Other (OTH)

AF:

0.999

AC:

2109

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.999

Hom.:

8128

Bravo

AF:

0.998

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 18, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.024

Mutation Taster

=300/0

polymorphism (auto)

(source)

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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rs5830914

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over