chr4-3518120-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002337.4(LRPAP1):c.665C>T(p.Thr222Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. T222P) has been classified as Uncertain significance.
Frequency
Consequence
NM_002337.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRPAP1 | NM_002337.4 | c.665C>T | p.Thr222Met | missense_variant | 5/8 | ENST00000650182.1 | |
LRPAP1 | NR_110005.2 | n.628C>T | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRPAP1 | ENST00000650182.1 | c.665C>T | p.Thr222Met | missense_variant | 5/8 | NM_002337.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250718Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135738
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461272Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 726950
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.665C>T (p.T222M) alteration is located in exon 5 (coding exon 5) of the LRPAP1 gene. This alteration results from a C to T substitution at nucleotide position 665, causing the threonine (T) at amino acid position 222 to be replaced by a methionine (M). 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