15-63127419-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032857.5(LACTB):āc.682A>Gā(p.Lys228Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 1,600,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032857.5 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 |
---|---|---|---|---|---|---|---|
LACTB | NM_032857.5 | c.682A>G | p.Lys228Glu | missense_variant | 4/6 | ENST00000261893.9 | |
LACTB | NM_171846.4 | c.682A>G | p.Lys228Glu | missense_variant | 4/5 | ||
LACTB | NM_001288585.2 | c.682A>G | p.Lys228Glu | missense_variant | 4/5 | ||
LACTB | XM_047432128.1 | c.682A>G | p.Lys228Glu | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LACTB | ENST00000261893.9 | c.682A>G | p.Lys228Glu | missense_variant | 4/6 | 1 | NM_032857.5 | P1 | |
LACTB | ENST00000413507.3 | c.682A>G | p.Lys228Glu | missense_variant | 4/5 | 1 | |||
LACTB | ENST00000557972.1 | c.205A>G | p.Lys69Glu | missense_variant | 3/3 | 2 | |||
RPS27L | ENST00000559763.1 | n.96-1399T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000753 AC: 18AN: 239124Hom.: 0 AF XY: 0.0000619 AC XY: 8AN XY: 129268
GnomAD4 exome AF: 0.0000324 AC: 47AN: 1448586Hom.: 0 Cov.: 30 AF XY: 0.0000305 AC XY: 22AN XY: 720132
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2023 | The c.682A>G (p.K228E) alteration is located in exon 4 (coding exon 4) of the LACTB gene. This alteration results from a A to G substitution at nucleotide position 682, causing the lysine (K) at amino acid position 228 to be replaced by a glutamic acid (E). 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