3-9941005-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001077415.3(CRELD1):c.616G>A(p.Ala206Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00038 in 1,614,190 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00039 ( 6 hom. )
Consequence
CRELD1
NM_001077415.3 missense
NM_001077415.3 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -0.294
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.007459134).
BP6
?
Variant 3-9941005-G-A is Benign according to our data. Variant chr3-9941005-G-A is described in ClinVar as [Benign]. Clinvar id is 414254.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRELD1 | NM_001077415.3 | c.616G>A | p.Ala206Thr | missense_variant | 6/11 | ENST00000452070.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRELD1 | ENST00000452070.6 | c.616G>A | p.Ala206Thr | missense_variant | 6/11 | 2 | NM_001077415.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152188Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00205 AC: 516AN: 251366Hom.: 5 AF XY: 0.00169 AC XY: 229AN XY: 135868
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GnomAD4 exome AF: 0.000390 AC: 570AN: 1461884Hom.: 6 Cov.: 33 AF XY: 0.000322 AC XY: 234AN XY: 727244
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GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152306Hom.: 0 Cov.: 31 AF XY: 0.000201 AC XY: 15AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Atrioventricular septal defect, susceptibility to, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;B
Vest4
MVP
MPC
0.16
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at