Variant 10-122836358-GAAAAA-GAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_022034.6(CUZD1):c.818-10_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 0.177 in 1,095,246 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., cov: 0)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

CUZD1
NM_022034.6 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.127

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 Benign. Variant got -10 ACMG points.

BP6

Variant 10-122836358-GAA-G is Benign according to our data. Variant chr10-122836358-GAA-G is described in ClinVar as [Benign]. Clinvar id is 402576.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
CUZD1	NM_022034.6 linkuse as main transcript	c.818-10_818-9del	splice_polypyrimidine_tract_variant, intron_variant	ENST00000392790.6	NP_071317.2
FAM24B-CUZD1	NR_037915.1 linkuse as main transcript	n.1494-10_1494-9del	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
CUZD1	NR_037912.2 linkuse as main transcript	n.681-10_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.818-10_818-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_022034.6	ENSP00000376540	P1	Q86UP6-1

Frequencies

GnomAD3 genomes

AF:

0.00246

AC:

346

AN:

140904

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00247

Gnomad ASJ

AF:

0.00328

Gnomad EAS

AF:

0.00144

Gnomad SAS

AF:

0.00113

Gnomad FIN

AF:

0.00979

Gnomad MID

AF:

0.00336

Gnomad NFE

AF:

0.00236

Gnomad OTH

AF:

0.00470

GnomAD3 exomes

AF:

0.296

AC:

21034

AN:

71052

Hom.:

AF XY:

0.293

AC XY:

11415

AN XY:

38914

show subpopulations

Gnomad AFR exome

AF:

0.300

Gnomad AMR exome

AF:

0.293

Gnomad ASJ exome

AF:

0.284

Gnomad EAS exome

AF:

0.273

Gnomad SAS exome

AF:

0.266

Gnomad FIN exome

AF:

0.285

Gnomad NFE exome

AF:

0.308

Gnomad OTH exome

AF:

0.289

GnomAD4 exome

AF:

0.203

AC:

194023

AN:

954342

Hom.:

AF XY:

0.206

AC XY:

96276

AN XY:

468494

show subpopulations

Gnomad4 AFR exome

AF:

0.206

Gnomad4 AMR exome

AF:

0.254

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.252

Gnomad4 SAS exome

AF:

0.209

Gnomad4 FIN exome

AF:

0.249

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.211

GnomAD4 genome

AF:

0.00249

AC:

351

AN:

140904

Hom.:

Cov.:

AF XY:

0.00324

AC XY:

220

AN XY:

67952

show subpopulations

Gnomad4 AFR

AF:

0.00131

Gnomad4 AMR

AF:

0.00246

Gnomad4 ASJ

AF:

0.00328

Gnomad4 EAS

AF:

0.00144

Gnomad4 SAS

AF:

0.00137

Gnomad4 FIN

AF:

0.00979

Gnomad4 NFE

AF:

0.00236

Gnomad4 OTH

AF:

0.00520

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over