19-55762699-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001145014.2(RFPL4A):c.388C>T(p.Gln130*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 150,654 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000047 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RFPL4A
NM_001145014.2 stop_gained
NM_001145014.2 stop_gained
Scores
1
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.63
Genes affected
RFPL4A (HGNC:16449): (ret finger protein like 4A) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be active in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000432 AC: 65AN: 150542Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000579 AC: 9AN: 155560Hom.: 0 AF XY: 0.0000364 AC XY: 3AN XY: 82478
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000468 AC: 65AN: 1389878Hom.: 0 Cov.: 71 AF XY: 0.0000467 AC XY: 32AN XY: 685544
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.000431 AC: 65AN: 150654Hom.: 0 Cov.: 33 AF XY: 0.000448 AC XY: 33AN XY: 73698
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at