chr9-26997770-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_022901.3(LRRC19):āc.553T>Cā(p.Phe185Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,611,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_022901.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC19 | NM_022901.3 | c.553T>C | p.Phe185Leu | missense_variant | 3/5 | ENST00000380055.6 | |
IFT74 | NM_025103.4 | c.587+7575A>G | intron_variant | ENST00000380062.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC19 | ENST00000380055.6 | c.553T>C | p.Phe185Leu | missense_variant | 3/5 | 1 | NM_022901.3 | P1 | |
IFT74 | ENST00000380062.10 | c.587+7575A>G | intron_variant | 1 | NM_025103.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152264Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000177 AC: 44AN: 248064Hom.: 0 AF XY: 0.000187 AC XY: 25AN XY: 134038
GnomAD4 exome AF: 0.000184 AC: 268AN: 1459130Hom.: 0 Cov.: 31 AF XY: 0.000172 AC XY: 125AN XY: 725740
GnomAD4 genome AF: 0.000112 AC: 17AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74390
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at