Variant 10-122836358-GA-G 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.818-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.99 ( 68530 hom., cov: 0)

Exomes 𝑓: 0.50 ( 9915 hom. )

Failed GnomAD Quality Control

Consequence

CUZD1
NM_022034.6 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.32

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-GA-G is Benign according to our data. Variant chr10-122836358-GA-G is described in ClinVar as [Benign]. Clinvar id is 402577.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.985

AC:

139112

AN:

141168

Hom.:

68536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.981

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.989

Gnomad ASJ

AF:

0.993

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.993

Gnomad FIN

AF:

0.949

Gnomad MID

AF:

0.997

Gnomad NFE

AF:

0.990

Gnomad OTH

AF:

0.982

GnomAD3 exomes

AF:

0.485

AC:

34442

AN:

71052

Hom.:

1076

AF XY:

0.483

AC XY:

18802

AN XY:

38914

show subpopulations

Gnomad AFR exome

AF:

0.486

Gnomad AMR exome

AF:

0.478

Gnomad ASJ exome

AF:

0.469

Gnomad EAS exome

AF:

0.471

Gnomad SAS exome

AF:

0.467

Gnomad FIN exome

AF:

0.502

Gnomad NFE exome

AF:

0.489

Gnomad OTH exome

AF:

0.482

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.502

AC:

535576

AN:

1067676

Hom.:

9915

Cov.:

AF XY:

0.500

AC XY:

261960

AN XY:

523626

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

0.478

Gnomad4 ASJ exome

AF:

0.492

Gnomad4 EAS exome

AF:

0.493

Gnomad4 SAS exome

AF:

0.481

Gnomad4 FIN exome

AF:

0.488

Gnomad4 NFE exome

AF:

0.504

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.985

AC:

139108

AN:

141172

Hom.:

68530

Cov.:

AF XY:

0.984

AC XY:

67000

AN XY:

68114

show subpopulations

Gnomad4 AFR

AF:

0.981

Gnomad4 AMR

AF:

0.989

Gnomad4 ASJ

AF:

0.993

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.993

Gnomad4 FIN

AF:

0.949

Gnomad4 NFE

AF:

0.990

Gnomad4 OTH

AF:

0.981

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