13-101453941-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004791.3(ITGBL1):āc.157G>Cā(p.Ala53Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000079 in 1,266,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 7.9e-7 ( 0 hom. )
Consequence
ITGBL1
NM_004791.3 missense
NM_004791.3 missense
Scores
1
8
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.08
Genes affected
ITGBL1 (HGNC:6164): (integrin subunit beta like 1) This gene encodes a beta integrin-related protein that is a member of the EGF-like protein family. The encoded protein contains integrin-like cysteine-rich repeats. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGBL1 | NM_004791.3 | c.157G>C | p.Ala53Pro | missense_variant | 2/11 | ENST00000376180.8 | |
ITGBL1 | NM_001271755.2 | c.157G>C | p.Ala53Pro | missense_variant | 2/10 | ||
ITGBL1 | NM_001271754.2 | c.-108+1010G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGBL1 | ENST00000376180.8 | c.157G>C | p.Ala53Pro | missense_variant | 2/11 | 1 | NM_004791.3 | P1 | |
ITGBL1 | ENST00000618057.4 | c.157G>C | p.Ala53Pro | missense_variant | 2/10 | 1 | |||
ITGBL1 | ENST00000545560.6 | c.-108+1010G>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.90e-7 AC: 1AN: 1266276Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 622046
GnomAD4 exome
AF:
AC:
1
AN:
1266276
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
622046
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T
Polyphen
0.99
.;D
Vest4
MutPred
Gain of catalytic residue at P57 (P = 0);Gain of catalytic residue at P57 (P = 0);
MVP
MPC
0.56
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
No publications associated with this variant yet.