rs138083875
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016343.4(CENPF):āc.7352A>Gā(p.Asn2451Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000824 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_016343.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPF | NM_016343.4 | c.7352A>G | p.Asn2451Ser | missense_variant | 13/20 | ENST00000366955.8 | NP_057427.3 | |
CENPF | XM_017000086.3 | c.7352A>G | p.Asn2451Ser | missense_variant | 13/20 | XP_016855575.1 | ||
CENPF | XM_011509082.4 | c.7352A>G | p.Asn2451Ser | missense_variant | 13/19 | XP_011507384.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPF | ENST00000366955.8 | c.7352A>G | p.Asn2451Ser | missense_variant | 13/20 | 1 | NM_016343.4 | ENSP00000355922.3 | ||
CENPF | ENST00000706765.1 | c.7352A>G | p.Asn2451Ser | missense_variant | 13/19 | ENSP00000516538.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251112Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135738
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461792Hom.: 0 Cov.: 34 AF XY: 0.0000976 AC XY: 71AN XY: 727200
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74322
ClinVar
Submissions by phenotype
Stromme syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 30, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 22, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at