chr5-96979923-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005575.3(LNPEP):āc.805A>Gā(p.Ser269Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,380 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.805A>G | p.Ser269Gly | missense_variant | 2/18 | ENST00000231368.10 | |
LNPEP | NM_175920.4 | c.763A>G | p.Ser255Gly | missense_variant | 2/18 | ||
LNPEP | XM_047417177.1 | c.805A>G | p.Ser269Gly | missense_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.805A>G | p.Ser269Gly | missense_variant | 2/18 | 1 | NM_005575.3 | P1 | |
LNPEP | ENST00000395770.3 | c.763A>G | p.Ser255Gly | missense_variant | 2/18 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249438Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134844
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460240Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 726266
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.805A>G (p.S269G) alteration is located in exon 2 (coding exon 2) of the LNPEP gene. This alteration results from a A to G substitution at nucleotide position 805, causing the serine (S) at amino acid position 269 to be replaced by a glycine (G). 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