19-41838913-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173506.7(LYPD4):c.179G>A(p.Gly60Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173506.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LYPD4 | ENST00000609812.6 | c.179G>A | p.Gly60Asp | missense_variant | Exon 3 of 5 | 1 | NM_173506.7 | ENSP00000476510.1 | ||
LYPD4 | ENST00000343055.5 | c.106+267G>A | intron_variant | Intron 3 of 4 | 1 | ENSP00000339568.4 | ||||
LYPD4 | ENST00000601246.5 | c.106+267G>A | intron_variant | Intron 4 of 5 | 5 | ENSP00000472570.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152070Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251360Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135850
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461816Hom.: 0 Cov.: 36 AF XY: 0.0000330 AC XY: 24AN XY: 727216
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 30 AF XY: 0.0000403 AC XY: 3AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.179G>A (p.G60D) alteration is located in exon 3 (coding exon 2) of the LYPD4 gene. This alteration results from a G to A substitution at nucleotide position 179, causing the glycine (G) at amino acid position 60 to be replaced by an aspartic acid (D). 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