chr14-99645268-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001127258.3(HHIPL1):c.61C>A(p.Pro21Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HHIPL1
NM_001127258.3 missense
NM_001127258.3 missense
Scores
7
8
3
Clinical Significance
Conservation
PhyloP100: 6.54
Publications
0 publications found
Genes affected
HHIPL1 (HGNC:19710): (HHIP like 1) This gene encodes a protein that belongs to the glucose/sorbosone dehydrogenase family. The encoded protein also contains a domain that binds folate and reduced folic acid derivatives. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.885
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001127258.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HHIPL1 | TSL:1 MANE Select | c.61C>A | p.Pro21Thr | missense | Exon 1 of 9 | ENSP00000330601.5 | Q96JK4-1 | ||
| HHIPL1 | TSL:1 | c.61C>A | p.Pro21Thr | missense | Exon 1 of 8 | ENSP00000349757.2 | Q96JK4-2 | ||
| HHIPL1 | c.61C>A | p.Pro21Thr | missense | Exon 1 of 9 | ENSP00000619076.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1266968Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 622048
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1266968
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
622048
African (AFR)
AF:
AC:
0
AN:
25482
American (AMR)
AF:
AC:
0
AN:
19728
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21036
East Asian (EAS)
AF:
AC:
0
AN:
27366
South Asian (SAS)
AF:
AC:
0
AN:
63624
European-Finnish (FIN)
AF:
AC:
0
AN:
32454
Middle Eastern (MID)
AF:
AC:
0
AN:
3666
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1021702
Other (OTH)
AF:
AC:
0
AN:
51910
GnomAD4 genome
GnomAD4 genome
Cov.:
34
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of helix (P = 0.062)
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
Publications
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