chr14-74101173-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001024674.3(LIN52):c.218C>T(p.Thr73Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000931 in 1,611,272 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 Uncertain significance (★).
Frequency
Consequence
NM_001024674.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIN52 | ENST00000555028.7 | c.218C>T | p.Thr73Met | missense_variant | Exon 5 of 6 | 1 | NM_001024674.3 | ENSP00000451812.2 | ||
LIN52 | ENST00000554938.2 | c.217+3313C>T | intron_variant | Intron 4 of 4 | 4 | ENSP00000452513.2 | ||||
LIN52 | ENST00000554076.5 | n.230C>T | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 | |||||
LIN52 | ENST00000553404.5 | n.822+3313C>T | intron_variant | Intron 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248754Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134598
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1458990Hom.: 0 Cov.: 30 AF XY: 0.00000689 AC XY: 5AN XY: 725798
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.230C>T (p.T77M) alteration is located in exon 5 (coding exon 5) of the LIN52 gene. This alteration results from a C to T substitution at nucleotide position 230, causing the threonine (T) at amino acid position 77 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at