chr10-122836358-GA-G

Variant names:

• chr10-122836358-GA-G
• rs11365591
• NM_022034.6:c.818-9delT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_022034.6(CUZD1):​c.818-9delT variant causes a 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 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000286088 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUZD1	NM_022034.6	c.818-9delT		intron_variant	Intron 5 of 8	ENST00000392790.6	NP_071317.2
CUZD1	NR_037912.2	n.681-9delT		intron_variant	Intron 4 of 7
FAM24B-CUZD1	NR_037915.1	n.1494-9delT		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUZD1	ENST00000392790.6	c.818-9delT		intron_variant	Intron 5 of 8	1	NM_022034.6	ENSP00000376540.1
ENSG00000286088	ENST00000368904.6	n.818-9delT		intron_variant	Intron 6 of 9	1		ENSP00000357900.2

Frequencies

GnomAD3 genomes AF: 0.985 AC: 139112 AN: 141168 Hom.: 68536 Cov.: 0

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

GnomAD2 exomes AF: 0.485 AC: 34442 AN: 71052 AF XY: 0.483

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 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.: 0 AF XY: 0.500 AC XY: 261960 AN XY: 523626

African (AFR) AF: 0.500 AC: 11061 AN: 22116

American (AMR) AF: 0.478 AC: 7828 AN: 16364

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 8216 AN: 16704

East Asian (EAS) AF: 0.493 AC: 14344 AN: 29114

South Asian (SAS) AF: 0.481 AC: 22514 AN: 46770

European-Finnish (FIN) AF: 0.488 AC: 16423 AN: 33642

Middle Eastern (MID) AF: 0.531 AC: 1930 AN: 3634

European-Non Finnish (NFE) AF: 0.504 AC: 431030 AN: 854912

Other (OTH) AF: 0.500 AC: 22230 AN: 44420

GnomAD4 genome AF: 0.985 AC: 139108 AN: 141172 Hom.: 68530 Cov.: 0 AF XY: 0.984 AC XY: 67000 AN XY: 68114

African (AFR) AF: 0.981 AC: 37605 AN: 38320

American (AMR) AF: 0.989 AC: 14065 AN: 14226

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3332 AN: 3354

East Asian (EAS) AF: 0.994 AC: 4827 AN: 4856

South Asian (SAS) AF: 0.993 AC: 4356 AN: 4388

European-Finnish (FIN) AF: 0.949 AC: 7630 AN: 8036

Middle Eastern (MID) AF: 0.996 AC: 271 AN: 272

European-Non Finnish (NFE) AF: 0.990 AC: 64235 AN: 64896

Other (OTH) AF: 0.981 AC: 1892 AN: 1928

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11365591; hg19: chr10-124595874;