4-3514817-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002337.4(LRPAP1):c.946C>T(p.Arg316Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R316H) has been classified as Likely benign.
Frequency
Consequence
NM_002337.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRPAP1 | NM_002337.4 | c.946C>T | p.Arg316Cys | missense_variant | 7/8 | ENST00000650182.1 | |
LRPAP1 | NR_110005.2 | n.909C>T | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRPAP1 | ENST00000650182.1 | c.946C>T | p.Arg316Cys | missense_variant | 7/8 | NM_002337.4 | P1 | ||
LRPAP1 | ENST00000296325.9 | n.909C>T | non_coding_transcript_exon_variant | 7/8 | 1 | ||||
LRPAP1 | ENST00000648517.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250706Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135684
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460938Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 726828
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152256Hom.: 0 Cov.: 35 AF XY: 0.0000134 AC XY: 1AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.946C>T (p.R316C) alteration is located in exon 7 (coding exon 7) of the LRPAP1 gene. This alteration results from a C to T substitution at nucleotide position 946, causing the arginine (R) at amino acid position 316 to be replaced by a cysteine (C). 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