14-20891649-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002935.3(RNASE3):c.-5-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000714 in 1,581,652 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000040 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000075 ( 0 hom. )
Consequence
RNASE3
NM_002935.3 intron
NM_002935.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.847
Genes affected
RNASE3 (HGNC:10046): (ribonuclease A family member 3) The protein encoded by this gene belongs to the pancreatic ribonuclease family, a subset of the ribonuclease A superfamily. The protein exhibits antimicrobial activity against pathogenic bacteria [provided by RefSeq, Oct 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNASE3 | NM_002935.3 | c.-5-33C>T | intron_variant | ENST00000304639.4 | |||
LOC100507513 | XR_110261.4 | n.723-15906G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNASE3 | ENST00000304639.4 | c.-5-33C>T | intron_variant | 1 | NM_002935.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000398 AC: 6AN: 150578Hom.: 0 Cov.: 30
GnomAD3 genomes
?
AF:
AC:
6
AN:
150578
Hom.:
Cov.:
30
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:
GnomAD3 exomes AF: 0.0000311 AC: 7AN: 225212Hom.: 0 AF XY: 0.0000248 AC XY: 3AN XY: 120800
GnomAD3 exomes
AF:
AC:
7
AN:
225212
Hom.:
AF XY:
AC XY:
3
AN XY:
120800
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000748 AC: 107AN: 1431074Hom.: 0 Cov.: 38 AF XY: 0.0000691 AC XY: 49AN XY: 709286
GnomAD4 exome
AF:
AC:
107
AN:
1431074
Hom.:
Cov.:
38
AF XY:
AC XY:
49
AN XY:
709286
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: 0.0000398 AC: 6AN: 150578Hom.: 0 Cov.: 30 AF XY: 0.0000272 AC XY: 2AN XY: 73486
GnomAD4 genome
?
AF:
AC:
6
AN:
150578
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
73486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at