17-76265611-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_182565.4(UBALD2):​c.106C>T​(p.His36Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

UBALD2
NM_182565.4 missense

Scores

4
9
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.49
Variant links:
Genes affected
UBALD2 (HGNC:28438): (UBA like domain containing 2)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UBALD2NM_182565.4 linkc.106C>T p.His36Tyr missense_variant Exon 1 of 3 ENST00000327490.8 NP_872371.1 Q8IYN6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBALD2ENST00000327490.8 linkc.106C>T p.His36Tyr missense_variant Exon 1 of 3 1 NM_182565.4 ENSP00000331298.6 Q8IYN6
UBALD2ENST00000587913.1 linkc.-61+208C>T intron_variant Intron 1 of 2 3 ENSP00000468297.1 K7ERK7
UBALD2ENST00000589240.1 linkc.-356C>T upstream_gene_variant 2 ENSP00000466518.1 K7EMI7

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1148806
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
567322
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Nov 24, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.106C>T (p.H36Y) alteration is located in exon 1 (coding exon 1) of the UBALD2 gene. This alteration results from a C to T substitution at nucleotide position 106, causing the histidine (H) at amino acid position 36 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.76
BayesDel_addAF
Uncertain
0.079
D
BayesDel_noAF
Benign
-0.12
CADD
Pathogenic
26
DANN
Uncertain
0.99
DEOGEN2
Benign
0.30
T
Eigen
Uncertain
0.27
Eigen_PC
Benign
0.21
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.96
D
M_CAP
Pathogenic
0.91
D
MetaRNN
Uncertain
0.63
D
MetaSVM
Benign
-0.59
T
MutationAssessor
Uncertain
2.3
M
PrimateAI
Pathogenic
0.85
D
PROVEAN
Pathogenic
-4.7
D
REVEL
Benign
0.22
Sift
Uncertain
0.0030
D
Sift4G
Uncertain
0.015
D
Polyphen
0.78
P
Vest4
0.53
MutPred
0.51
Loss of disorder (P = 0.2692);
MVP
0.29
MPC
2.0
ClinPred
0.99
D
GERP RS
2.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.73
gMVP
0.94

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-74261692; API