2-80302637-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000295057.4(LRRTM1):c.1183G>A(p.Ala395Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000361 in 1,607,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000295057.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRTM1 | NM_178839.5 | c.1183G>A | p.Ala395Thr | missense_variant | 2/2 | ENST00000295057.4 | NP_849161.2 | |
CTNNA2 | NM_001282597.3 | c.1057-90574C>T | intron_variant | ENST00000402739.9 | NP_001269526.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRTM1 | ENST00000295057.4 | c.1183G>A | p.Ala395Thr | missense_variant | 2/2 | 1 | NM_178839.5 | ENSP00000295057 | P1 | |
CTNNA2 | ENST00000402739.9 | c.1057-90574C>T | intron_variant | 1 | NM_001282597.3 | ENSP00000384638 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000458 AC: 11AN: 240022Hom.: 0 AF XY: 0.0000381 AC XY: 5AN XY: 131330
GnomAD4 exome AF: 0.0000261 AC: 38AN: 1455042Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 723690
GnomAD4 genome AF: 0.000131 AC: 20AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2024 | The c.1183G>A (p.A395T) alteration is located in exon 2 (coding exon 1) of the LRRTM1 gene. This alteration results from a G to A substitution at nucleotide position 1183, causing the alanine (A) at amino acid position 395 to be replaced by a threonine (T). 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