3-172648098-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020792.6(NCEH1):c.155A>G(p.Tyr52Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,613,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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.155A>G | p.Tyr52Cys | missense_variant | 2/5 | ENST00000475381.7 | |
NCEH1 | NM_001146276.3 | c.155A>G | p.Tyr52Cys | missense_variant | 2/5 | ||
NCEH1 | NM_001146277.3 | c.-235A>G | 5_prime_UTR_variant | 2/5 | |||
NCEH1 | NM_001146278.3 | c.-32-2406A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCEH1 | ENST00000475381.7 | c.155A>G | p.Tyr52Cys | missense_variant | 2/5 | 1 | NM_020792.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251212Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135750
GnomAD4 exome AF: 0.0000978 AC: 143AN: 1461888Hom.: 0 Cov.: 34 AF XY: 0.000100 AC XY: 73AN XY: 727248
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.251A>G (p.Y84C) alteration is located in exon 2 (coding exon 2) of the NCEH1 gene. This alteration results from a A to G substitution at nucleotide position 251, causing the tyrosine (Y) at amino acid position 84 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