10-67097690-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_178011.5(LRRTM3):c.1640C>T(p.Thr547Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,612,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178011.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRTM3 | NM_178011.5 | c.1640C>T | p.Thr547Met | missense_variant | 3/3 | ENST00000361320.5 | |
CTNNA3 | NM_013266.4 | c.1047+82627G>A | intron_variant | ENST00000433211.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRTM3 | ENST00000361320.5 | c.1640C>T | p.Thr547Met | missense_variant | 3/3 | 1 | NM_178011.5 | P1 | |
CTNNA3 | ENST00000433211.7 | c.1047+82627G>A | intron_variant | 1 | NM_013266.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151796Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250984Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135630
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460708Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726694
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151796Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74114
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | The c.1640C>T (p.T547M) alteration is located in exon 3 (coding exon 3) of the LRRTM3 gene. This alteration results from a C to T substitution at nucleotide position 1640, causing the threonine (T) at amino acid position 547 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