5-192178-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080478.3(LRRC14B):c.640C>T(p.Arg214Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,600,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080478.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC14B | NM_001080478.3 | c.640C>T | p.Arg214Cys | missense_variant | 1/2 | ENST00000328278.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC14B | ENST00000328278.4 | c.640C>T | p.Arg214Cys | missense_variant | 1/2 | 1 | NM_001080478.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 6AN: 215774Hom.: 0 AF XY: 0.0000337 AC XY: 4AN XY: 118752
GnomAD4 exome AF: 0.000135 AC: 196AN: 1448256Hom.: 0 Cov.: 32 AF XY: 0.000140 AC XY: 101AN XY: 719248
GnomAD4 genome AF: 0.000105 AC: 16AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2023 | The c.640C>T (p.R214C) alteration is located in exon 1 (coding exon 1) of the LRRC14B gene. This alteration results from a C to T substitution at nucleotide position 640, causing the arginine (R) at amino acid position 214 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