6-160545505-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005577.4(LPA):āc.5333A>Gā(p.Asn1778Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005577.4 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 | UniProt |
---|---|---|---|---|---|---|---|
LPA | NM_005577.4 | c.5333A>G | p.Asn1778Ser | missense_variant | 33/39 | ENST00000316300.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPA | ENST00000316300.10 | c.5333A>G | p.Asn1778Ser | missense_variant | 33/39 | 1 | NM_005577.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151910Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251438Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135896
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461290Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727010
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151910Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.5333A>G (p.N1778S) alteration is located in exon 34 (coding exon 33) of the LPA gene. This alteration results from a A to G substitution at nucleotide position 5333, causing the asparagine (N) at amino acid position 1778 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