2-175941013-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001305009.1(LNPK):c.774G>A(p.Ser258Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000998 in 453,078 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00084 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
LNPK
NM_001305009.1 synonymous
NM_001305009.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.36
Genes affected
LNPK (HGNC:21610): (lunapark, ER junction formation factor) Enables identical protein binding activity. Involved in endoplasmic reticulum tubular network maintenance and positive regulation of endoplasmic reticulum tubular network organization. Located in endoplasmic reticulum tubular network membrane and nucleoplasm. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant 2-175941013-C-T is Benign according to our data. Variant chr2-175941013-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651553.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.36 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000836 (127/151914) while in subpopulation NFE AF= 0.000913 (62/67944). AF 95% confidence interval is 0.00073. There are 0 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LNPK | ENST00000544803.5 | c.774G>A | p.Ser258Ser | synonymous_variant | Exon 10 of 14 | 1 | ENSP00000440905.1 | |||
LNPK | ENST00000272748.9 | c.707-1356G>A | intron_variant | Intron 9 of 12 | 1 | NM_030650.3 | ENSP00000272748.4 | |||
LNPK | ENST00000409660.5 | c.338-1356G>A | intron_variant | Intron 7 of 10 | 1 | ENSP00000386237.1 | ||||
LNPK | ENST00000431754.1 | n.32-1356G>A | intron_variant | Intron 1 of 3 | 5 | ENSP00000388507.1 |
Frequencies
GnomAD3 genomes AF: 0.000837 AC: 127AN: 151794Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00147 AC: 184AN: 125036Hom.: 2 AF XY: 0.00147 AC XY: 101AN XY: 68580
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GnomAD4 exome AF: 0.00108 AC: 325AN: 301164Hom.: 2 Cov.: 0 AF XY: 0.000990 AC XY: 170AN XY: 171694
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GnomAD4 genome AF: 0.000836 AC: 127AN: 151914Hom.: 0 Cov.: 31 AF XY: 0.000781 AC XY: 58AN XY: 74252
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
LNPK: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at