3-172647949-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020792.6(NCEH1):c.304G>A(p.Glu102Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000861 in 1,614,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCEH1 | NM_020792.6 | c.304G>A | p.Glu102Lys | missense_variant | 2/5 | ENST00000475381.7 | |
NCEH1 | NM_001146276.3 | c.304G>A | p.Glu102Lys | missense_variant | 2/5 | ||
NCEH1 | NM_001146277.3 | c.-86G>A | 5_prime_UTR_variant | 2/5 | |||
NCEH1 | NM_001146278.3 | c.-32-2257G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCEH1 | ENST00000475381.7 | c.304G>A | p.Glu102Lys | missense_variant | 2/5 | 1 | NM_020792.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251394Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135874
GnomAD4 exome AF: 0.0000807 AC: 118AN: 1461892Hom.: 0 Cov.: 34 AF XY: 0.0000784 AC XY: 57AN XY: 727246
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2023 | The c.400G>A (p.E134K) alteration is located in exon 2 (coding exon 2) of the NCEH1 gene. This alteration results from a G to A substitution at nucleotide position 400, causing the glutamic acid (E) at amino acid position 134 to be replaced by a lysine (K). 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