chr3-120335948-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000295628.4(LRRC58):āc.506A>Gā(p.Glu169Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00446 in 1,574,298 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0031 ( 1 hom., cov: 33)
Exomes š: 0.0046 ( 25 hom. )
Consequence
LRRC58
ENST00000295628.4 missense
ENST00000295628.4 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 7.10
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.05185336).
BP6
Variant 3-120335948-T-C is Benign according to our data. Variant chr3-120335948-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2654060.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 25 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC58 | NM_001099678.2 | c.506A>G | p.Glu169Gly | missense_variant | 2/4 | ENST00000295628.4 | NP_001093148.1 | |
LRRC58 | XM_047447401.1 | c.*49A>G | 3_prime_UTR_variant | 3/3 | XP_047303357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC58 | ENST00000295628.4 | c.506A>G | p.Glu169Gly | missense_variant | 2/4 | 1 | NM_001099678.2 | ENSP00000295628.3 |
Frequencies
GnomAD3 genomes AF: 0.00315 AC: 479AN: 152032Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00305 AC: 733AN: 240514Hom.: 2 AF XY: 0.00289 AC XY: 377AN XY: 130660
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GnomAD4 exome AF: 0.00460 AC: 6548AN: 1422148Hom.: 25 Cov.: 27 AF XY: 0.00437 AC XY: 3101AN XY: 708996
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GnomAD4 genome AF: 0.00315 AC: 479AN: 152150Hom.: 1 Cov.: 33 AF XY: 0.00286 AC XY: 213AN XY: 74402
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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 | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | LRRC58: BS2 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at