rs3745526
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_171557.1(C19orf48P):n.78A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 451,572 control chromosomes in the GnomAD database, including 21,197 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 6189 hom., cov: 33)
Exomes 𝑓: 0.30 ( 15008 hom. )
Consequence
C19orf48P
NR_171557.1 non_coding_transcript_exon
NR_171557.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.00
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C19orf48P | NR_171557.1 | n.78A>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C19orf48P | ENST00000641834.2 | n.477A>T | non_coding_transcript_exon_variant | 4/4 | |||||
C19orf48P | ENST00000641539.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 39974AN: 151720Hom.: 6181 Cov.: 33
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GnomAD4 exome AF: 0.302 AC: 90401AN: 299734Hom.: 15008 Cov.: 0 AF XY: 0.308 AC XY: 51744AN XY: 168160
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GnomAD4 genome ? AF: 0.263 AC: 39996AN: 151838Hom.: 6189 Cov.: 33 AF XY: 0.270 AC XY: 20036AN XY: 74216
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at