Variant rs11365591 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022034.6(CUZD1):c.818-13_818-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,206,800 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00025 ( 0 hom. )

Consequence

CUZD1
NM_022034.6 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

CUZD1 (HGNC:17937): (CUB and zona pellucida like domains 1) Predicted to be involved in trypsinogen activation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CUZD1 links:

FAM24B-CUZD1 (HGNC:):

FAM24B-CUZD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
CUZD1	NM_022034.6 linkuse as main transcript	c.818-13_818-9del	splice_polypyrimidine_tract_variant, intron_variant	ENST00000392790.6	NP_071317.2
FAM24B-CUZD1	NR_037915.1 linkuse as main transcript	n.1494-13_1494-9del	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
CUZD1	NR_037912.2 linkuse as main transcript	n.681-13_681-9del	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUZD1	ENST00000392790.6 linkuse as main transcript	c.818-13_818-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_022034.6	ENSP00000376540	P1	Q86UP6-1

Frequencies

GnomAD3 genomes

AF:

0.0000142

AC:

AN:

141026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000125

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000154

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000943

AC:

AN:

71052

Hom.:

AF XY:

0.00111

AC XY:

AN XY:

38914

show subpopulations

Gnomad AFR exome

AF:

0.000779

Gnomad AMR exome

AF:

0.000790

Gnomad ASJ exome

AF:

0.000408

Gnomad EAS exome

AF:

0.000583

Gnomad SAS exome

AF:

0.00123

Gnomad FIN exome

AF:

0.000553

Gnomad NFE exome

AF:

0.00112

Gnomad OTH exome

AF:

0.000667

GnomAD4 exome

AF:

0.000247

AC:

263

AN:

1065774

Hom.:

AF XY:

0.000285

AC XY:

149

AN XY:

522704

show subpopulations

Gnomad4 AFR exome

AF:

0.000226

Gnomad4 AMR exome

AF:

0.000551

Gnomad4 ASJ exome

AF:

0.000300

Gnomad4 EAS exome

AF:

0.000241

Gnomad4 SAS exome

AF:

0.000750

Gnomad4 FIN exome

AF:

0.000477

Gnomad4 NFE exome

AF:

0.000204

Gnomad4 OTH exome

AF:

0.000248

GnomAD4 genome

AF:

0.0000142

AC:

AN:

141026

Hom.:

Cov.:

AF XY:

0.0000147

AC XY:

AN XY:

67998

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000125

Gnomad4 NFE

AF:

0.0000154

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over