rs151080979
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_201550.4(LRRC10):āc.584T>Cā(p.Ile195Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00552 in 1,614,190 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0039 ( 1 hom., cov: 33)
Exomes š: 0.0057 ( 29 hom. )
Consequence
LRRC10
NM_201550.4 missense
NM_201550.4 missense
Scores
4
10
4
Clinical Significance
Conservation
PhyloP100: 9.25
Genes affected
LRRC10 (HGNC:20264): (leucine rich repeat containing 10) Predicted to enable actin binding activity. Predicted to be involved in cardiac muscle cell development. Predicted to be located in myofibril. Predicted to be active in cytoskeleton and sarcomere. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.012428105).
BP6
?
Variant 12-69610255-A-G is Benign according to our data. Variant chr12-69610255-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 478141.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 29 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC10 | NM_201550.4 | c.584T>C | p.Ile195Thr | missense_variant | 1/1 | ENST00000361484.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC10 | ENST00000361484.5 | c.584T>C | p.Ile195Thr | missense_variant | 1/1 | NM_201550.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00392 AC: 596AN: 152198Hom.: 1 Cov.: 33
GnomAD3 genomes
?
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33
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GnomAD3 exomes AF: 0.00491 AC: 1234AN: 251418Hom.: 5 AF XY: 0.00498 AC XY: 677AN XY: 135888
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GnomAD4 exome AF: 0.00569 AC: 8311AN: 1461874Hom.: 29 Cov.: 31 AF XY: 0.00568 AC XY: 4130AN XY: 727236
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GnomAD4 genome ? AF: 0.00390 AC: 594AN: 152316Hom.: 1 Cov.: 33 AF XY: 0.00438 AC XY: 326AN XY: 74490
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ExAC
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678
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | LRRC10: BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 14, 2019 | This variant is associated with the following publications: (PMID: 29431102) - |
Dilated Cardiomyopathy, Dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
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