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12-101291762-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014503.3(UTP20):c.912C>T(p.His304=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00778 in 1,599,170 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 55 hom., cov: 32)
Exomes 𝑓: 0.0067 ( 81 hom. )

Consequence

UTP20
NM_014503.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.127
Variant links:
Genes affected
UTP20 (HGNC:17897): (UTP20 small subunit processome component) UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and is involved in 18S rRNA processing (Wang et al., 2007 [PubMed 17498821]).[supplied by OMIM, Jun 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-101291762-C-T is Benign according to our data. Variant chr12-101291762-C-T is described in ClinVar as [Benign]. Clinvar id is 782221.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.127 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0184 (2798/152244) while in subpopulation AFR AF= 0.0478 (1983/41526). AF 95% confidence interval is 0.046. There are 55 homozygotes in gnomad4. There are 1335 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 51 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UTP20NM_014503.3 linkuse as main transcriptc.912C>T p.His304= synonymous_variant 9/62 ENST00000261637.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UTP20ENST00000261637.5 linkuse as main transcriptc.912C>T p.His304= synonymous_variant 9/621 NM_014503.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0182
AC:
2773
AN:
152126
Hom.:
51
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0473
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0179
Gnomad ASJ
AF:
0.0164
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00538
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00579
Gnomad OTH
AF:
0.0249
GnomAD3 exomes
AF:
0.00907
AC:
2176
AN:
239926
Hom.:
21
AF XY:
0.00851
AC XY:
1100
AN XY:
129270
show subpopulations
Gnomad AFR exome
AF:
0.0502
Gnomad AMR exome
AF:
0.00930
Gnomad ASJ exome
AF:
0.0178
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00534
Gnomad FIN exome
AF:
0.000472
Gnomad NFE exome
AF:
0.00625
Gnomad OTH exome
AF:
0.0103
GnomAD4 exome
AF:
0.00666
AC:
9640
AN:
1446926
Hom.:
81
Cov.:
30
AF XY:
0.00655
AC XY:
4708
AN XY:
718444
show subpopulations
Gnomad4 AFR exome
AF:
0.0491
Gnomad4 AMR exome
AF:
0.0108
Gnomad4 ASJ exome
AF:
0.0175
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00571
Gnomad4 FIN exome
AF:
0.000452
Gnomad4 NFE exome
AF:
0.00532
Gnomad4 OTH exome
AF:
0.0103
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0184
AC:
2798
AN:
152244
Hom.:
55
Cov.:
32
AF XY:
0.0179
AC XY:
1335
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0478
Gnomad4 AMR
AF:
0.0178
Gnomad4 ASJ
AF:
0.0164
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00559
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.00582
Gnomad4 OTH
AF:
0.0246
Alfa
AF:
0.00933
Hom.:
12
Bravo
AF:
0.0220
Asia WGS
AF:
0.00779
AC:
27
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
0.62
Dann
Benign
0.21
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs75817013; hg19: chr12-101685540; API