5-170259003-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005565.5(LCP2):c.958-125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 648,196 control chromosomes in the GnomAD database, including 79,842 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005565.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCP2 | ENST00000046794.10 | c.958-125A>G | intron_variant | Intron 14 of 20 | 1 | NM_005565.5 | ENSP00000046794.5 | |||
LCP2 | ENST00000521416.5 | c.343-125A>G | intron_variant | Intron 6 of 12 | 2 | ENSP00000428871.1 | ||||
LCP2 | ENST00000520344.1 | c.259-125A>G | intron_variant | Intron 5 of 7 | 5 | ENSP00000430391.1 |
Frequencies
GnomAD3 genomes AF: 0.506 AC: 76885AN: 151944Hom.: 19569 Cov.: 32
GnomAD4 exome AF: 0.489 AC: 242600AN: 496134Hom.: 60259 AF XY: 0.487 AC XY: 129603AN XY: 266376
GnomAD4 genome AF: 0.506 AC: 76941AN: 152062Hom.: 19583 Cov.: 32 AF XY: 0.512 AC XY: 38033AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 21% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at