chr11-100061207-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_014361.4(CNTN5):c.981-5C>T 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 0.000244 in 1,603,276 control chromosomes in the GnomAD database, including 5 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
NM_014361.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNTN5 | NM_014361.4 | c.981-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000524871.6 | |||
LOC105369456 | XR_947948.3 | n.208-5677G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNTN5 | ENST00000524871.6 | c.981-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014361.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152112Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000534 AC: 132AN: 247114Hom.: 1 AF XY: 0.000746 AC XY: 100AN XY: 134080
GnomAD4 exome AF: 0.000258 AC: 375AN: 1451046Hom.: 5 Cov.: 30 AF XY: 0.000376 AC XY: 271AN XY: 720196
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | CNTN5: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at