5-140631963-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000591.4(CD14):c.1021G>A(p.Glu341Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,613,654 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000591.4 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 |
---|---|---|---|---|---|---|---|
CD14 | NM_000591.4 | c.1021G>A | p.Glu341Lys | missense_variant | 2/2 | ENST00000302014.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD14 | ENST00000302014.11 | c.1021G>A | p.Glu341Lys | missense_variant | 2/2 | 1 | NM_000591.4 | P1 | |
CD14 | ENST00000498971.7 | c.1021G>A | p.Glu341Lys | missense_variant | 3/3 | 2 | P1 | ||
CD14 | ENST00000512545.2 | c.1021G>A | p.Glu341Lys | missense_variant | 3/3 | 3 | P1 | ||
CD14 | ENST00000519715.2 | c.1021G>A | p.Glu341Lys | missense_variant | 3/3 | 4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00128 AC: 195AN: 152178Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000355 AC: 89AN: 250960Hom.: 1 AF XY: 0.000250 AC XY: 34AN XY: 135732
GnomAD4 exome AF: 0.000141 AC: 206AN: 1461358Hom.: 0 Cov.: 32 AF XY: 0.000110 AC XY: 80AN XY: 726888
GnomAD4 genome ? AF: 0.00128 AC: 195AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00133 AC XY: 99AN XY: 74462
ClinVar
Submissions by phenotype
CD14-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 28, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at