22-50503411-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000474879.7(LMF2):āc.2104A>Cā(p.Thr702Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000621 in 1,609,896 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 (ā ).
Frequency
Consequence
ENST00000474879.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMF2 | NM_033200.3 | c.2104A>C | p.Thr702Pro | missense_variant | 14/14 | ENST00000474879.7 | NP_149977.2 | |
LMF2 | NM_001363816.2 | c.2029A>C | p.Thr677Pro | missense_variant | 14/14 | NP_001350745.1 | ||
LMF2 | XM_006724426.4 | c.1939A>C | p.Thr647Pro | missense_variant | 13/13 | XP_006724489.1 | ||
LMF2 | XM_047441593.1 | c.1102A>C | p.Thr368Pro | missense_variant | 9/9 | XP_047297549.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMF2 | ENST00000474879.7 | c.2104A>C | p.Thr702Pro | missense_variant | 14/14 | 1 | NM_033200.3 | ENSP00000424381.1 | ||
LMF2 | ENST00000216080.5 | c.2029A>C | p.Thr677Pro | missense_variant | 14/14 | 2 | ENSP00000216080.5 | |||
LMF2 | ENST00000504717.1 | n.1083A>C | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242772Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132764
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457842Hom.: 0 Cov.: 29 AF XY: 0.00000827 AC XY: 6AN XY: 725368
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152054Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.2104A>C (p.T702P) alteration is located in exon 14 (coding exon 14) of the LMF2 gene. This alteration results from a A to C substitution at nucleotide position 2104, causing the threonine (T) at amino acid position 702 to be replaced by a proline (P). 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