chr8-55946456-A-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_002350.4(LYN):āc.141A>Cā(p.Glu47Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,608,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. E47E) has been classified as Likely benign.
Frequency
Consequence
NM_002350.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LYN | NM_002350.4 | c.141A>C | p.Glu47Asp | missense_variant | 3/13 | ENST00000519728.6 | |
LYN | NM_001111097.3 | c.78A>C | p.Glu26Asp | missense_variant | 3/13 | ||
LYN | XM_011517529.4 | c.-127A>C | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYN | ENST00000519728.6 | c.141A>C | p.Glu47Asp | missense_variant | 3/13 | 1 | NM_002350.4 | P4 | |
LYN | ENST00000520220.6 | c.78A>C | p.Glu26Asp | missense_variant | 3/13 | 1 | A1 | ||
LYN | ENST00000520050.1 | c.141A>C | p.Glu47Asp | missense_variant | 3/6 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249720Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135216
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1456596Hom.: 0 Cov.: 28 AF XY: 0.0000221 AC XY: 16AN XY: 725086
GnomAD4 genome AF: 0.0000459 AC: 7AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74502
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2023 | ClinVar contains an entry for this variant (Variation ID: 1366165). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with LYN-related conditions. This variant is present in population databases (rs145665634, gnomAD 0.006%). This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 47 of the LYN protein (p.Glu47Asp). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at