6-160541120-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_005577.4(LPA):c.5581C>T(p.His1861Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005577.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251350Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135880
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727206
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5581C>T (p.H1861Y) alteration is located in exon 36 (coding exon 35) of the LPA gene. This alteration results from a C to T substitution at nucleotide position 5581, causing the histidine (H) at amino acid position 1861 to be replaced by a tyrosine (Y). 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