19-19201711-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003721.4(RFXANK):c.775C>T(p.Pro259Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003721.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RFXANK | NM_003721.4 | c.775C>T | p.Pro259Ser | missense_variant | Exon 10 of 10 | ENST00000303088.9 | NP_003712.1 | |
NR2C2AP | NM_176880.6 | c.*214G>A | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000331552.12 | NP_795361.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RFXANK | ENST00000303088.9 | c.775C>T | p.Pro259Ser | missense_variant | Exon 10 of 10 | 1 | NM_003721.4 | ENSP00000305071.2 | ||
NR2C2AP | ENST00000331552 | c.*214G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_176880.6 | ENSP00000332823.6 | |||
NR2C2AP | ENST00000420605.7 | c.415-148G>A | intron_variant | Intron 5 of 5 | 2 | ENSP00000402756.1 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000176 AC: 44AN: 250550Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135514
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1461738Hom.: 0 Cov.: 31 AF XY: 0.0000825 AC XY: 60AN XY: 727180
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
MHC class II deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at