1-87340153-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_006769.4(LMO4):āc.440A>Gā(p.Asn147Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,614,040 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 (ā ).
Frequency
Consequence
NM_006769.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMO4 | NM_006769.4 | c.440A>G | p.Asn147Ser | missense_variant | 4/5 | ENST00000370544.10 | NP_006760.1 | |
LMO4 | NM_001369491.1 | c.440A>G | p.Asn147Ser | missense_variant | 4/5 | NP_001356420.1 | ||
LMO4 | XM_047432941.1 | c.440A>G | p.Asn147Ser | missense_variant | 5/6 | XP_047288897.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMO4 | ENST00000370544.10 | c.440A>G | p.Asn147Ser | missense_variant | 4/5 | 1 | NM_006769.4 | ENSP00000359575.4 | ||
LMO4 | ENST00000370542.1 | c.440A>G | p.Asn147Ser | missense_variant | 4/5 | 1 | ENSP00000359573.1 | |||
LMO4 | ENST00000489303.1 | n.675A>G | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251458Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135902
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727234
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.440A>G (p.N147S) alteration is located in exon 4 (coding exon 3) of the LMO4 gene. This alteration results from a A to G substitution at nucleotide position 440, causing the asparagine (N) at amino acid position 147 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