6-53899787-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018214.5(LRRC1):c.683C>G(p.Ser228Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000359 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018214.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC1 | ENST00000370888.6 | c.683C>G | p.Ser228Cys | missense_variant | Exon 8 of 14 | 1 | NM_018214.5 | ENSP00000359925.1 | ||
LRRC1 | ENST00000487251.5 | n.*85C>G | non_coding_transcript_exon_variant | Exon 9 of 11 | 2 | ENSP00000435217.1 | ||||
LRRC1 | ENST00000487251.5 | n.*85C>G | 3_prime_UTR_variant | Exon 9 of 11 | 2 | ENSP00000435217.1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000212 AC: 53AN: 249520Hom.: 0 AF XY: 0.000229 AC XY: 31AN XY: 135378
GnomAD4 exome AF: 0.000367 AC: 536AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.000341 AC XY: 248AN XY: 727218
GnomAD4 genome AF: 0.000283 AC: 43AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.683C>G (p.S228C) alteration is located in exon 8 (coding exon 8) of the LRRC1 gene. This alteration results from a C to G substitution at nucleotide position 683, causing the serine (S) at amino acid position 228 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at