rs61732016
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_016343.4(CENPF):c.6844A>G(p.Met2282Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,614,182 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Likely benign (★★).
Frequency
Consequence
NM_016343.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPF | NM_016343.4 | c.6844A>G | p.Met2282Val | missense_variant | Exon 13 of 20 | ENST00000366955.8 | NP_057427.3 | |
CENPF | XM_017000086.3 | c.6844A>G | p.Met2282Val | missense_variant | Exon 13 of 20 | XP_016855575.1 | ||
CENPF | XM_011509082.4 | c.6844A>G | p.Met2282Val | missense_variant | Exon 13 of 19 | XP_011507384.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CENPF | ENST00000366955.8 | c.6844A>G | p.Met2282Val | missense_variant | Exon 13 of 20 | 1 | NM_016343.4 | ENSP00000355922.3 | ||
CENPF | ENST00000706765.1 | c.6844A>G | p.Met2282Val | missense_variant | Exon 13 of 19 | ENSP00000516538.1 |
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 234AN: 152228Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000415 AC: 104AN: 250882Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135604
GnomAD4 exome AF: 0.000179 AC: 261AN: 1461836Hom.: 1 Cov.: 34 AF XY: 0.000164 AC XY: 119AN XY: 727228
GnomAD4 genome AF: 0.00154 AC: 235AN: 152346Hom.: 3 Cov.: 33 AF XY: 0.00140 AC XY: 104AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at