chr3-45595219-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014240.3(LIMD1):c.340C>T(p.Pro114Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000187 in 1,602,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014240.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIMD1 | NM_014240.3 | c.340C>T | p.Pro114Ser | missense_variant | 1/8 | ENST00000273317.5 | NP_055055.1 | |
LIMD1 | XM_011534207.4 | c.340C>T | p.Pro114Ser | missense_variant | 1/2 | XP_011532509.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIMD1 | ENST00000273317.5 | c.340C>T | p.Pro114Ser | missense_variant | 1/8 | 1 | NM_014240.3 | ENSP00000273317 | P1 | |
LIMD1 | ENST00000440097.5 | c.340C>T | p.Pro114Ser | missense_variant | 1/6 | 5 | ENSP00000394537 | |||
LIMD1 | ENST00000465039.5 | n.102-17673C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1450168Hom.: 0 Cov.: 35 AF XY: 0.00000139 AC XY: 1AN XY: 720026
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.340C>T (p.P114S) alteration is located in exon 1 (coding exon 1) of the LIMD1 gene. This alteration results from a C to T substitution at nucleotide position 340, causing the proline (P) at amino acid position 114 to be replaced by a serine (S). 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