15-100574025-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001040616.3(LINS1):c.848T>A(p.Met283Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001040616.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINS1 | NM_001040616.3 | c.848T>A | p.Met283Lys | missense_variant | 5/7 | ENST00000314742.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINS1 | ENST00000314742.13 | c.848T>A | p.Met283Lys | missense_variant | 5/7 | 5 | NM_001040616.3 | P1 | |
LINS1 | ENST00000561308.5 | c.848T>A | p.Met283Lys | missense_variant | 5/5 | 1 | |||
LINS1 | ENST00000560133.5 | c.491T>A | p.Met164Lys | missense_variant | 5/5 | 2 | |||
LINS1 | ENST00000559149.5 | n.1005T>A | non_coding_transcript_exon_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251154Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135790
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461690Hom.: 0 Cov.: 36 AF XY: 0.0000151 AC XY: 11AN XY: 727114
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 02, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at