chr8-55946443-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002350.4(LYN):c.133-5C>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 0.0000169 in 1,598,742 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_002350.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYN | NM_002350.4 | c.133-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000519728.6 | |||
LYN | NM_001111097.3 | c.70-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
LYN | XM_011517529.4 | c.-135-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYN | ENST00000519728.6 | c.133-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002350.4 | P4 | |||
LYN | ENST00000520220.6 | c.70-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
LYN | ENST00000520050.1 | c.133-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249866Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135274
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1446624Hom.: 0 Cov.: 28 AF XY: 0.0000166 AC XY: 12AN XY: 720838
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at