chr13-27556336-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_153371.4(LNX2):c.1446C>T(p.Thr482=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 1,613,920 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 27 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 22 hom. )
Consequence
LNX2
NM_153371.4 synonymous
NM_153371.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.26
Genes affected
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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=-0.61).
BP6
?
Variant 13-27556336-G-A is Benign according to our data. Variant chr13-27556336-G-A is described in ClinVar as [Benign]. Clinvar id is 776786.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.26 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1530/152166) while in subpopulation AFR AF= 0.0314 (1302/41514). AF 95% confidence interval is 0.0299. There are 27 homozygotes in gnomad4. There are 748 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 27 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LNX2 | NM_153371.4 | c.1446C>T | p.Thr482= | synonymous_variant | 7/10 | ENST00000316334.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LNX2 | ENST00000316334.5 | c.1446C>T | p.Thr482= | synonymous_variant | 7/10 | 1 | NM_153371.4 | P1 | |
LNX2 | ENST00000649248.1 | c.1446C>T | p.Thr482= | synonymous_variant | 8/11 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1530AN: 152048Hom.: 27 Cov.: 32
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GnomAD3 exomes AF: 0.00340 AC: 853AN: 250940Hom.: 5 AF XY: 0.00264 AC XY: 358AN XY: 135600
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GnomAD4 exome AF: 0.00171 AC: 2498AN: 1461754Hom.: 22 Cov.: 31 AF XY: 0.00160 AC XY: 1165AN XY: 727180
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GnomAD4 genome ? AF: 0.0101 AC: 1530AN: 152166Hom.: 27 Cov.: 32 AF XY: 0.0101 AC XY: 748AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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