8-55946471-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002350.4(LYN):āc.156T>Cā(p.Pro52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,458,376 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P52P) has been classified as Likely benign.
Frequency
Consequence
NM_002350.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYN | NM_002350.4 | c.156T>C | p.Pro52= | synonymous_variant | 3/13 | ENST00000519728.6 | |
LYN | NM_001111097.3 | c.93T>C | p.Pro31= | synonymous_variant | 3/13 | ||
LYN | XM_011517529.4 | c.-112T>C | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYN | ENST00000519728.6 | c.156T>C | p.Pro52= | synonymous_variant | 3/13 | 1 | NM_002350.4 | P4 | |
LYN | ENST00000520220.6 | c.93T>C | p.Pro31= | synonymous_variant | 3/13 | 1 | A1 | ||
LYN | ENST00000520050.1 | c.156T>C | p.Pro52= | synonymous_variant | 3/6 | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249502Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135082
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1458376Hom.: 0 Cov.: 28 AF XY: 0.0000207 AC XY: 15AN XY: 725740
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at