rs140389574
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_201550.4(LRRC10):c.206C>T(p.Pro69Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,614,046 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P69P) has been classified as Likely benign.
Frequency
Consequence
NM_201550.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC10 | NM_201550.4 | c.206C>T | p.Pro69Leu | missense_variant | 1/1 | ENST00000361484.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC10 | ENST00000361484.5 | c.206C>T | p.Pro69Leu | missense_variant | 1/1 | NM_201550.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000644 AC: 98AN: 152194Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00254 AC: 637AN: 251122Hom.: 9 AF XY: 0.00340 AC XY: 461AN XY: 135708
GnomAD4 exome AF: 0.00117 AC: 1714AN: 1461734Hom.: 23 Cov.: 31 AF XY: 0.00169 AC XY: 1226AN XY: 727156
GnomAD4 genome ? AF: 0.000663 AC: 101AN: 152312Hom.: 2 Cov.: 33 AF XY: 0.00103 AC XY: 77AN XY: 74474
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2020 | This variant is associated with the following publications: (PMID: 28032242) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at