1-154237115-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014847.4(UBAP2L):​c.682T>G​(p.Phe228Val) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F228L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

UBAP2L
NM_014847.4 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.90
Variant links:
Genes affected
UBAP2L (HGNC:29877): (ubiquitin associated protein 2 like) Enables RNA binding activity. Involved in binding activity of sperm to zona pellucida and stress granule assembly. Acts upstream of or within hematopoietic stem cell homeostasis. Part of PcG protein complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09338707).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UBAP2LNM_014847.4 linkc.682T>G p.Phe228Val missense_variant Exon 8 of 27 ENST00000428931.6 NP_055662.3 Q14157-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBAP2LENST00000428931.6 linkc.682T>G p.Phe228Val missense_variant Exon 8 of 27 5 NM_014847.4 ENSP00000389445.1 Q14157-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461768
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727186
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33468
American (AMR)
AF:
0.00
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
26132
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39690
South Asian (SAS)
AF:
0.00
AC:
0
AN:
86250
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53414
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
8.99e-7
AC:
1
AN:
1111930
Other (OTH)
AF:
0.00
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
22
DANN
Benign
0.97
DEOGEN2
Benign
0.17
.;.;T;T;T;T;T;T;T
Eigen
Benign
-0.19
Eigen_PC
Benign
0.059
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Benign
0.78
T;T;T;T;D;D;D;D;.
M_CAP
Benign
0.0078
T
MetaRNN
Benign
0.093
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.40
N;.;N;.;.;.;.;.;N
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-1.3
N;.;N;N;N;N;N;N;N
REVEL
Benign
0.034
Sift
Benign
0.31
T;.;T;T;T;T;T;T;T
Sift4G
Benign
0.50
T;T;T;T;T;T;T;T;T
Polyphen
0.0090
B;B;B;B;.;.;.;.;B
Vest4
0.14
MutPred
0.14
Gain of glycosylation at T225 (P = 0.1595);.;Gain of glycosylation at T225 (P = 0.1595);.;Gain of glycosylation at T225 (P = 0.1595);.;.;Gain of glycosylation at T225 (P = 0.1595);Gain of glycosylation at T225 (P = 0.1595);
MVP
0.11
MPC
0.89
ClinPred
0.36
T
GERP RS
5.7
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.12
gMVP
0.26
Mutation Taster
=79/21
polymorphism

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: rs770563723; hg19: chr1-154209591; API