rs3823994
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_022143.5(LRRC4):āc.837T>Cā(p.Ser279=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S279S) has been classified as Benign.
Frequency
Consequence
NM_022143.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC4 | NM_022143.5 | c.837T>C | p.Ser279= | synonymous_variant | 2/2 | ENST00000249363.4 | |
SND1 | NM_014390.4 | c.1779+38748A>G | intron_variant | ENST00000354725.8 | |||
LRRC4 | XM_011516461.4 | c.837T>C | p.Ser279= | synonymous_variant | 3/3 | ||
LRRC4 | XM_047420695.1 | c.837T>C | p.Ser279= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC4 | ENST00000249363.4 | c.837T>C | p.Ser279= | synonymous_variant | 2/2 | 1 | NM_022143.5 | P1 | |
SND1 | ENST00000354725.8 | c.1779+38748A>G | intron_variant | 1 | NM_014390.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152018Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250930Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135780
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461478Hom.: 0 Cov.: 38 AF XY: 0.00000413 AC XY: 3AN XY: 727044
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74392
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at