Variant rs9878047 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001077415.3(CRELD1):c.1048+258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,601,580 control chromosomes in the GnomAD database, including 66,497 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 13936 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52561 hom. )

Consequence

CRELD1
NM_001077415.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.882

Variant links:

Genes affected

CRELD1 (HGNC:14630): (cysteine rich with EGF like domains 1) This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

CRELD1 links:

(HGNC:):

links:

PRRT3 (HGNC:26591): (proline rich transmembrane protein 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PRRT3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-9943773-T-C is Benign according to our data. Variant chr3-9943773-T-C is described in ClinVar as [Benign]. Clinvar id is 1276154.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-9943773-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRELD1	NM_001077415.3 linkuse as main transcript	c.1048+258T>C		intron_variant		ENST00000452070.6	NP_001070883.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRELD1	ENST00000452070.6 linkuse as main transcript	c.1048+258T>C		intron_variant		2	NM_001077415.3	ENSP00000393643	P1	Q96HD1-1

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55946

AN:

151960

Hom.:

13918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.715

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.279

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.151

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.325

GnomAD4 exome

AF:

0.257

AC:

371885

AN:

1449502

Hom.:

52561

Cov.:

AF XY:

0.255

AC XY:

183745

AN XY:

720684

show subpopulations

Gnomad4 AFR exome

AF:

0.735

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.295

Gnomad4 EAS exome

AF:

0.223

Gnomad4 SAS exome

AF:

0.261

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.368

AC:

56012

AN:

152078

Hom.:

13936

Cov.:

AF XY:

0.358

AC XY:

26601

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.715

Gnomad4 AMR

AF:

0.279

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.151

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.266

Hom.:

6155

Bravo

AF:

0.396

Asia WGS

AF:

0.233

AC:

812

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.10

DANN

Benign

0.28

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