3-172633518-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020792.6(NCEH1):c.1184G>A(p.Arg395Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020792.6 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 |
---|---|---|---|---|---|---|---|
NCEH1 | NM_020792.6 | c.1184G>A | p.Arg395Gln | missense_variant | 5/5 | ENST00000475381.7 | |
NCEH1 | NM_001146276.3 | c.1208G>A | p.Arg403Gln | missense_variant | 5/5 | ||
NCEH1 | NM_001146277.3 | c.785G>A | p.Arg262Gln | missense_variant | 5/5 | ||
NCEH1 | NM_001146278.3 | c.785G>A | p.Arg262Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCEH1 | ENST00000475381.7 | c.1184G>A | p.Arg395Gln | missense_variant | 5/5 | 1 | NM_020792.6 | P1 | |
NCEH1 | ENST00000538775.5 | c.1304G>A | p.Arg435Gln | missense_variant | 5/5 | 2 | |||
NCEH1 | ENST00000543711.5 | c.785G>A | p.Arg262Gln | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251358Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135848
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727208
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.1304G>A (p.R435Q) alteration is located in exon 5 (coding exon 5) of the NCEH1 gene. This alteration results from a G to A substitution at nucleotide position 1304, causing the arginine (R) at amino acid position 435 to be replaced by a glutamine (Q). 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