3-9940761-A-AAGGGAGAGGGAG

Position:

• chr3-9940761-A-AAGGGAGAGGGAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001077415.3(CRELD1):​c.461-75_461-64dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.081 (1253 hom., cov: 20)
  • Exomes 𝑓: 0.052 (2786 hom.)
  • Failed GnomAD Quality Control
• Consequence: CRELD1 NM_001077415.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.128

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]

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-9940761-A-AAGGGAGAGGGAG is Benign according to our data. Variant chr3-9940761-A-AAGGGAGAGGGAG is described in ClinVar as [Benign]. Clinvar id is 1229493.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRELD1	NM_001077415.3	c.461-75_461-64dup		intron_variant		ENST00000452070.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRELD1	ENST00000452070.6	c.461-75_461-64dup		intron_variant		2	NM_001077415.3	P1

Frequencies

GnomAD3 genomes AF: 0.0811 AC: 8431 AN: 103894 Hom.: 1251 Cov.: 20

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0179

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0846

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0583

Gnomad NFE AF: 0.0359

Gnomad OTH AF: 0.0787

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0518 AC: 38170 AN: 736346 Hom.: 2786 AF XY: 0.0496 AC XY: 19014 AN XY: 383674

Gnomad4 AFR exome AF: 0.437

Gnomad4 AMR exome AF: 0.0600

Gnomad4 ASJ exome AF: 0.127

Gnomad4 EAS exome AF: 0.000237

Gnomad4 SAS exome AF: 0.0149

Gnomad4 FIN exome AF: 0.0363

Gnomad4 NFE exome AF: 0.0426

Gnomad4 OTH exome AF: 0.0785

GnomAD4 genome AF: 0.0812 AC: 8444 AN: 103958 Hom.: 1253 Cov.: 20 AF XY: 0.0766 AC XY: 3851 AN XY: 50286

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.0846

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00612

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0359

Gnomad4 OTH AF: 0.0775

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs376951607; hg19: chr3-9982445;