3-172711074-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000538775.5(NCEH1):c.7A>C(p.Ser3Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,607,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000538775.5 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 | upstream_gene_variant | ENST00000475381.7 | ||||
NCEH1 | NM_001146276.3 | upstream_gene_variant | |||||
NCEH1 | NM_001146277.3 | upstream_gene_variant | |||||
NCEH1 | NM_001146278.3 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCEH1 | ENST00000475381.7 | upstream_gene_variant | 1 | NM_020792.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246408Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134188
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1455304Hom.: 0 Cov.: 33 AF XY: 0.0000180 AC XY: 13AN XY: 722746
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.7A>C (p.S3R) alteration is located in exon 1 (coding exon 1) of the NCEH1 gene. This alteration results from a A to C substitution at nucleotide position 7, causing the serine (S) at amino acid position 3 to be replaced by an arginine (R). 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