chr5-96979552-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_005575.3(LNPEP):āc.434A>Cā(p.Asn145Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,990 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 (ā ).
Frequency
Consequence
NM_005575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.434A>C | p.Asn145Thr | missense_variant | 2/18 | ENST00000231368.10 | |
LNPEP | NM_175920.4 | c.392A>C | p.Asn131Thr | missense_variant | 2/18 | ||
LNPEP | XM_047417177.1 | c.434A>C | p.Asn145Thr | missense_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.434A>C | p.Asn145Thr | missense_variant | 2/18 | 1 | NM_005575.3 | P1 | |
LNPEP | ENST00000395770.3 | c.392A>C | p.Asn131Thr | missense_variant | 2/18 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250890Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135586
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461810Hom.: 0 Cov.: 33 AF XY: 0.0000468 AC XY: 34AN XY: 727208
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.434A>C (p.N145T) alteration is located in exon 2 (coding exon 2) of the LNPEP gene. This alteration results from a A to C substitution at nucleotide position 434, causing the asparagine (N) at amino acid position 145 to be replaced by a threonine (T). 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