rs2233860
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000304639.4(RNASE3):c.*16G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,594,758 control chromosomes in the GnomAD database, including 31,128 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 0.19 ( 3286 hom., cov: 30)
Exomes 𝑓: 0.19 ( 27842 hom. )
Consequence
RNASE3
ENST00000304639.4 3_prime_UTR
ENST00000304639.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.110
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 Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNASE3 | NM_002935.3 | c.*16G>C | 3_prime_UTR_variant | 2/2 | ENST00000304639.4 | NP_002926.2 | ||
LOC100507513 | XR_110261.4 | n.723-16442C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNASE3 | ENST00000304639.4 | c.*16G>C | 3_prime_UTR_variant | 2/2 | 1 | NM_002935.3 | ENSP00000302324 | P1 |
Frequencies
GnomAD3 genomes AF: 0.191 AC: 28803AN: 150504Hom.: 3281 Cov.: 30
GnomAD3 genomes
AF:
AC:
28803
AN:
150504
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: 0.177 AC: 41617AN: 235548Hom.: 4239 AF XY: 0.180 AC XY: 22740AN XY: 126594
GnomAD3 exomes
AF:
AC:
41617
AN:
235548
Hom.:
AF XY:
AC XY:
22740
AN XY:
126594
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: 0.192 AC: 276647AN: 1444136Hom.: 27842 Cov.: 35 AF XY: 0.191 AC XY: 136947AN XY: 716930
GnomAD4 exome
AF:
AC:
276647
AN:
1444136
Hom.:
Cov.:
35
AF XY:
AC XY:
136947
AN XY:
716930
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: 0.191 AC: 28819AN: 150622Hom.: 3286 Cov.: 30 AF XY: 0.189 AC XY: 13938AN XY: 73622
GnomAD4 genome
AF:
AC:
28819
AN:
150622
Hom.:
Cov.:
30
AF XY:
AC XY:
13938
AN XY:
73622
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:
Asia WGS
AF:
AC:
453
AN:
3478
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