chr10-95595157-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000398190.2(RPS3AP36):n.560C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.466 in 759,106 control chromosomes in the GnomAD database, including 88,666 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 0.39 ( 14440 hom., cov: 33)
Exomes 𝑓: 0.48 ( 74226 hom. )
Consequence
RPS3AP36
ENST00000398190.2 non_coding_transcript_exon
ENST00000398190.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.65
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS3AP36 | ENST00000398190.2 | n.560C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.394 AC: 59954AN: 152018Hom.: 14441 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
59954
AN:
152018
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.484 AC: 293583AN: 606970Hom.: 74226 Cov.: 4 AF XY: 0.476 AC XY: 157761AN XY: 331606
GnomAD4 exome
AF:
AC:
293583
AN:
606970
Hom.:
Cov.:
4
AF XY:
AC XY:
157761
AN XY:
331606
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.394 AC: 59953AN: 152136Hom.: 14440 Cov.: 33 AF XY: 0.393 AC XY: 29239AN XY: 74362
GnomAD4 genome
?
AF:
AC:
59953
AN:
152136
Hom.:
Cov.:
33
AF XY:
AC XY:
29239
AN XY:
74362
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at