rs56172264
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000551295.7(CNTN1):c.804-8A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,612,208 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000551295.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CNTN1 | NM_001843.4 | c.804-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000551295.7 | NP_001834.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTN1 | ENST00000551295.7 | c.804-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001843.4 | ENSP00000447006 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00103 AC: 157AN: 151984Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00125 AC: 313AN: 250000Hom.: 0 AF XY: 0.00129 AC XY: 174AN XY: 135150
GnomAD4 exome AF: 0.00126 AC: 1843AN: 1460106Hom.: 2 Cov.: 31 AF XY: 0.00130 AC XY: 945AN XY: 726378
GnomAD4 genome AF: 0.00103 AC: 157AN: 152102Hom.: 2 Cov.: 32 AF XY: 0.000914 AC XY: 68AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 18, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Compton-North congenital myopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at