NM_000538.4:c.297G>C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000538.4(RFXAP):c.297G>C(p.Pro99Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,548,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P99P) has been classified as Likely benign.
Frequency
Consequence
NM_000538.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000660 AC: 10AN: 151456Hom.: 0 AF XY: 0.0000743 AC XY: 6AN XY: 80768
GnomAD4 exome AF: 0.0000430 AC: 60AN: 1396368Hom.: 0 Cov.: 31 AF XY: 0.0000421 AC XY: 29AN XY: 688246
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74436
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