19-43802374-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001031749.3(LYPD5):c.7A>G(p.Met3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,551,634 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 (★).
Frequency
Consequence
NM_001031749.3 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 |
---|---|---|---|---|---|---|---|
LYPD5 | NM_001031749.3 | c.7A>G | p.Met3Val | missense_variant | 1/5 | ENST00000377950.8 | |
LYPD5 | NM_182573.3 | c.-65-2540A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LYPD5 | ENST00000377950.8 | c.7A>G | p.Met3Val | missense_variant | 1/5 | 1 | NM_001031749.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000895 AC: 14AN: 156402Hom.: 0 AF XY: 0.000109 AC XY: 9AN XY: 82906
GnomAD4 exome AF: 0.0000264 AC: 37AN: 1399370Hom.: 0 Cov.: 34 AF XY: 0.0000232 AC XY: 16AN XY: 690194
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152264Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.7A>G (p.M3V) alteration is located in exon 1 (coding exon 1) of the LYPD5 gene. This alteration results from a A to G substitution at nucleotide position 7, causing the methionine (M) at amino acid position 3 to be replaced by a valine (V). 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