2-175964387-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_030650.3(LNPK):c.478G>A(p.Ala160Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,204 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030650.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LNPK | ENST00000272748.9 | c.478G>A | p.Ala160Thr | missense_variant | Exon 8 of 13 | 1 | NM_030650.3 | ENSP00000272748.4 | ||
LNPK | ENST00000544803.5 | c.478G>A | p.Ala160Thr | missense_variant | Exon 8 of 14 | 1 | ENSP00000440905.1 | |||
LNPK | ENST00000409660.5 | c.109G>A | p.Ala37Thr | missense_variant | Exon 6 of 11 | 1 | ENSP00000386237.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 251066Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135654
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1460938Hom.: 1 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 726832
GnomAD4 genome AF: 0.000112 AC: 17AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74466
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.478G>A (p.A160T) alteration is located in exon 8 (coding exon 7) of the LNPK gene. This alteration results from a G to A substitution at nucleotide position 478, causing the alanine (A) at amino acid position 160 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