chr3-2571548-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_175607.3(CNTN4):c.45G>C(p.Leu15Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00235 in 1,613,036 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 39 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 37 hom. )
Consequence
CNTN4
NM_175607.3 missense
NM_175607.3 missense
Scores
1
15
Clinical Significance
Conservation
PhyloP100: 4.03
Genes affected
CNTN4 (HGNC:2174): (contactin 4) This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0057327747).
BP6
?
Variant 3-2571548-G-C is Benign according to our data. Variant chr3-2571548-G-C is described in ClinVar as [Benign]. Clinvar id is 783213.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1814/152318) while in subpopulation AFR AF= 0.0415 (1723/41562). AF 95% confidence interval is 0.0398. There are 39 homozygotes in gnomad4. There are 866 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1787 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN4 | NM_175607.3 | c.45G>C | p.Leu15Phe | missense_variant | 4/25 | ENST00000418658.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN4 | ENST00000418658.6 | c.45G>C | p.Leu15Phe | missense_variant | 4/25 | 5 | NM_175607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0117 AC: 1787AN: 152200Hom.: 36 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00312 AC: 777AN: 249326Hom.: 12 AF XY: 0.00234 AC XY: 316AN XY: 135260
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GnomAD4 exome AF: 0.00135 AC: 1972AN: 1460718Hom.: 37 Cov.: 30 AF XY: 0.00121 AC XY: 879AN XY: 726768
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GnomAD4 genome ? AF: 0.0119 AC: 1814AN: 152318Hom.: 39 Cov.: 33 AF XY: 0.0116 AC XY: 866AN XY: 74482
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464
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;.;.;T;T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.0
.;.;B;B;.;B
Vest4
0.38, 0.35, 0.35
MutPred
Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP
MPC
0.12
ClinPred
T
GERP RS
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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