8-144520530-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014665.4(LRRC14):c.622C>T(p.Arg208Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,599,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC14 | NM_014665.4 | c.622C>T | p.Arg208Cys | missense_variant | 3/4 | ENST00000292524.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC14 | ENST00000292524.6 | c.622C>T | p.Arg208Cys | missense_variant | 3/4 | 1 | NM_014665.4 | P1 | |
LRRC14 | ENST00000529022.5 | c.622C>T | p.Arg208Cys | missense_variant | 4/5 | 1 | P1 | ||
LRRC14 | ENST00000527730.1 | c.622C>T | p.Arg208Cys | missense_variant | 3/3 | 2 | |||
LRRC14 | ENST00000531310.1 | n.1077C>T | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152248Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000251 AC: 6AN: 238812Hom.: 0 AF XY: 0.0000383 AC XY: 5AN XY: 130534
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1447454Hom.: 0 Cov.: 32 AF XY: 0.0000167 AC XY: 12AN XY: 720666
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152248Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.622C>T (p.R208C) alteration is located in exon 3 (coding exon 2) of the LRRC14 gene. This alteration results from a C to T substitution at nucleotide position 622, causing the arginine (R) at amino acid position 208 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