chr3-9934531-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001077415.3(CRELD1):c.93C>T(p.Pro31=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000476 in 1,614,090 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00034 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00049 ( 4 hom. )
Consequence
CRELD1
NM_001077415.3 synonymous
NM_001077415.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.135
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 3-9934531-C-T is Benign according to our data. Variant chr3-9934531-C-T is described in ClinVar as [Benign]. Clinvar id is 1615675.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.135 with no splicing effect.
BS2
High AC in GnomAd4 at 52 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRELD1 | NM_001077415.3 | c.93C>T | p.Pro31= | synonymous_variant | 2/11 | ENST00000452070.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRELD1 | ENST00000452070.6 | c.93C>T | p.Pro31= | synonymous_variant | 2/11 | 2 | NM_001077415.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152172Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000844 AC: 212AN: 251152Hom.: 3 AF XY: 0.00104 AC XY: 141AN XY: 135838
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GnomAD4 exome AF: 0.000490 AC: 716AN: 1461800Hom.: 4 Cov.: 33 AF XY: 0.000628 AC XY: 457AN XY: 727206
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GnomAD4 genome AF: 0.000341 AC: 52AN: 152290Hom.: 1 Cov.: 32 AF XY: 0.000416 AC XY: 31AN XY: 74474
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | CRELD1: BS1, BS2 - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Atrioventricular septal defect, susceptibility to, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 20, 2023 | - - |
Computational scores
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Benign
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at