chr8-144518144-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014665.4(LRRC14):c.-112+103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0093 in 161,572 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 11 hom., cov: 34)
Exomes 𝑓: 0.0033 ( 0 hom. )
Consequence
LRRC14
NM_014665.4 intron
NM_014665.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.50
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 8-144518144-C-T is Benign according to our data. Variant chr8-144518144-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1187315.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00967 (1471/152068) while in subpopulation AFR AF= 0.0276 (1145/41494). AF 95% confidence interval is 0.0263. There are 11 homozygotes in gnomad4. There are 704 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC14 | NM_014665.4 | c.-112+103C>T | intron_variant | ENST00000292524.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC14 | ENST00000292524.6 | c.-112+103C>T | intron_variant | 1 | NM_014665.4 | P1 | |||
LRRC14 | ENST00000529022.5 | c.-179+103C>T | intron_variant | 1 | P1 | ||||
LRRC14 | ENST00000527730.1 | c.-26+103C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00956 AC: 1453AN: 151960Hom.: 9 Cov.: 34
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GnomAD4 exome AF: 0.00326 AC: 31AN: 9504Hom.: 0 AF XY: 0.00253 AC XY: 13AN XY: 5138
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GnomAD4 genome ? AF: 0.00967 AC: 1471AN: 152068Hom.: 11 Cov.: 34 AF XY: 0.00947 AC XY: 704AN XY: 74326
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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
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2019 | - - |
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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at