5-140632692-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000591.4(CD14):c.292G>T(p.Ala98Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000591.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD14 | NM_000591.4 | c.292G>T | p.Ala98Ser | missense_variant | 2/2 | ENST00000302014.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD14 | ENST00000302014.11 | c.292G>T | p.Ala98Ser | missense_variant | 2/2 | 1 | NM_000591.4 | P1 | |
CD14 | ENST00000498971.7 | c.292G>T | p.Ala98Ser | missense_variant | 3/3 | 2 | P1 | ||
CD14 | ENST00000512545.2 | c.292G>T | p.Ala98Ser | missense_variant | 3/3 | 3 | P1 | ||
CD14 | ENST00000519715.2 | c.292G>T | p.Ala98Ser | missense_variant | 3/3 | 4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000643 AC: 16AN: 248992Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135274
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461480Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727064
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.292G>T (p.A98S) alteration is located in exon 3 (coding exon 2) of the CD14 gene. This alteration results from a G to T substitution at nucleotide position 292, causing the alanine (A) at amino acid position 98 to be replaced by a serine (S). 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