chr7-2559184-G-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_152558.5(IQCE):c.3G>T(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000094 in 1,064,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 9.4e-7 ( 0 hom. )
Consequence
IQCE
NM_152558.5 start_lost
NM_152558.5 start_lost
Scores
2
6
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.79
Publications
0 publications found
Genes affected
IQCE (HGNC:29171): (IQ motif containing E) Involved in limb morphogenesis. Predicted to be extrinsic component of membrane. Predicted to be part of plasma membrane protein complex. [provided by Alliance of Genome Resources, Apr 2022]
IQCE Gene-Disease associations (from GenCC):
- postaxial polydactyly type AInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- polydactyly, postaxial, type a7Inheritance: AR Classification: LIMITED Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 1 pathogenic variants. Next in-frame start position is after 66 codons. Genomic position: 2571591. Lost 0.094 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 9.40e-7 AC: 1AN: 1064276Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 502610 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1064276
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
502610
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22184
American (AMR)
AF:
AC:
0
AN:
7808
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13428
East Asian (EAS)
AF:
AC:
0
AN:
25106
South Asian (SAS)
AF:
AC:
0
AN:
19448
European-Finnish (FIN)
AF:
AC:
0
AN:
21762
Middle Eastern (MID)
AF:
AC:
0
AN:
2878
European-Non Finnish (NFE)
AF:
AC:
1
AN:
909306
Other (OTH)
AF:
AC:
0
AN:
42356
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D
MetaSVM
Benign
T
PhyloP100
PROVEAN
Benign
N;N;N;.;N;.
REVEL
Benign
Sift
Uncertain
D;D;D;.;D;.
Sift4G
Uncertain
T;D;D;D;D;D
Polyphen
B;.;B;.;.;.
Vest4
MutPred
Gain of catalytic residue at M1 (P = 0.01);Gain of catalytic residue at M1 (P = 0.01);Gain of catalytic residue at M1 (P = 0.01);Gain of catalytic residue at M1 (P = 0.01);Gain of catalytic residue at M1 (P = 0.01);Gain of catalytic residue at M1 (P = 0.01);
MVP
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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