chr3-326074-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006614.4(CHL1):c.197+10G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,555,454 control chromosomes in the GnomAD database, including 52,972 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.35 ( 14431 hom., cov: 32)
Exomes 𝑓: 0.21 ( 38541 hom. )
Consequence
CHL1
NM_006614.4 intron
NM_006614.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0960
Genes affected
CHL1 (HGNC:1939): (cell adhesion molecule L1 like) The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 3-326074-G-C is Benign according to our data. Variant chr3-326074-G-C is described in ClinVar as [Benign]. Clinvar id is 1676925.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHL1 | NM_006614.4 | c.197+10G>C | intron_variant | ENST00000256509.7 | NP_006605.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHL1 | ENST00000256509.7 | c.197+10G>C | intron_variant | 1 | NM_006614.4 | ENSP00000256509 | P3 |
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52653AN: 151724Hom.: 14381 Cov.: 32
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GnomAD3 exomes AF: 0.209 AC: 51471AN: 246746Hom.: 8634 AF XY: 0.202 AC XY: 26985AN XY: 133508
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GnomAD4 exome AF: 0.212 AC: 298008AN: 1403612Hom.: 38541 Cov.: 23 AF XY: 0.210 AC XY: 147292AN XY: 701592
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GnomAD4 genome AF: 0.347 AC: 52760AN: 151842Hom.: 14431 Cov.: 32 AF XY: 0.336 AC XY: 24971AN XY: 74210
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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 | GeneDx | Apr 12, 2022 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
CHL1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
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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