chr18-6093388-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001330559.2(L3MBTL4):āc.1340A>Gā(p.Asn447Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,611,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001330559.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L3MBTL4 | NM_001330559.2 | c.1340A>G | p.Asn447Ser | missense_variant | 15/19 | ENST00000317931.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L3MBTL4 | ENST00000317931.12 | c.1340A>G | p.Asn447Ser | missense_variant | 15/19 | 5 | NM_001330559.2 | P4 | |
L3MBTL4 | ENST00000400104.7 | c.1340A>G | p.Asn447Ser | missense_variant | 15/17 | 1 | |||
ENST00000659442.1 | n.1423+4038T>C | intron_variant, non_coding_transcript_variant | |||||||
L3MBTL4 | ENST00000400105.6 | c.1340A>G | p.Asn447Ser | missense_variant | 15/20 | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 43AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000644 AC: 16AN: 248392Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134260
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1459266Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 725850
GnomAD4 genome AF: 0.000276 AC: 42AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.1340A>G (p.N447S) alteration is located in exon 15 (coding exon 13) of the L3MBTL4 gene. This alteration results from a A to G substitution at nucleotide position 1340, causing the asparagine (N) at amino acid position 447 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