rs11949052

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000389100.9(RNF180):​c.1-91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 1,088,848 control chromosomes in the GnomAD database, including 5,858 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 0.076 ( 636 hom., cov: 32)
Exomes 𝑓: 0.10 ( 5222 hom. )

Consequence

RNF180
ENST00000389100.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.697
Variant links:
Genes affected
RNF180 (HGNC:27752): (ring finger protein 180) Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to be involved in norepinephrine metabolic process; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and serotonin metabolic process. Predicted to act upstream of or within several processes, including adult behavior; positive regulation of protein ubiquitination; and protein polyubiquitination. Predicted to be located in nuclear envelope. Predicted to be integral component of membrane. Predicted to be intrinsic component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNF180NM_001113561.2 linkuse as main transcriptc.1-91G>A intron_variant ENST00000389100.9 NP_001107033.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF180ENST00000389100.9 linkuse as main transcriptc.1-91G>A intron_variant 1 NM_001113561.2 ENSP00000373752 P1Q86T96-1
RNF180ENST00000296615.10 linkuse as main transcriptc.1-91G>A intron_variant 1 ENSP00000296615 Q86T96-2
RNF180ENST00000504296.1 linkuse as main transcriptc.1-91G>A intron_variant 3 ENSP00000426884

Frequencies

GnomAD3 genomes
AF:
0.0765
AC:
11634
AN:
152098
Hom.:
639
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0197
Gnomad AMI
AF:
0.212
Gnomad AMR
AF:
0.0670
Gnomad ASJ
AF:
0.0802
Gnomad EAS
AF:
0.000577
Gnomad SAS
AF:
0.0550
Gnomad FIN
AF:
0.0950
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.116
Gnomad OTH
AF:
0.0755
GnomAD4 exome
AF:
0.100
AC:
93692
AN:
936632
Hom.:
5222
AF XY:
0.0988
AC XY:
47163
AN XY:
477234
show subpopulations
Gnomad4 AFR exome
AF:
0.0177
Gnomad4 AMR exome
AF:
0.0494
Gnomad4 ASJ exome
AF:
0.0906
Gnomad4 EAS exome
AF:
0.000280
Gnomad4 SAS exome
AF:
0.0577
Gnomad4 FIN exome
AF:
0.0950
Gnomad4 NFE exome
AF:
0.116
Gnomad4 OTH exome
AF:
0.0905
GnomAD4 genome
AF:
0.0764
AC:
11627
AN:
152216
Hom.:
636
Cov.:
32
AF XY:
0.0748
AC XY:
5570
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0197
Gnomad4 AMR
AF:
0.0670
Gnomad4 ASJ
AF:
0.0802
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.0547
Gnomad4 FIN
AF:
0.0950
Gnomad4 NFE
AF:
0.116
Gnomad4 OTH
AF:
0.0747
Alfa
AF:
0.102
Hom.:
868
Bravo
AF:
0.0718
Asia WGS
AF:
0.0250
AC:
86
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.48
DANN
Benign
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11949052; hg19: chr5-63496544; API