3-9934817-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_001077415.3(CRELD1):c.175-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,606,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
CRELD1
NM_001077415.3 intron
NM_001077415.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.131
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 -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 3-9934817-C-T is Benign according to our data. Variant chr3-9934817-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3712520.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 5 AD gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRELD1 | NM_001077415.3 | c.175-18C>T | intron_variant | Intron 2 of 10 | ENST00000452070.6 | NP_001070883.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRELD1 | ENST00000452070.6 | c.175-18C>T | intron_variant | Intron 2 of 10 | 2 | NM_001077415.3 | ENSP00000393643.2 | |||
ENSG00000288550 | ENST00000683484.1 | n.1400-18C>T | intron_variant | Intron 16 of 23 | ENSP00000507040.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000415 AC: 1AN: 241094Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130366
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GnomAD4 exome AF: 0.00000344 AC: 5AN: 1453748Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 722588
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Atrioventricular septal defect, susceptibility to, 2 Benign:1
Apr 22, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at