NM_004791.3:c.317G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 1P and 16B. PP3BP6_Very_StrongBS1BS2
The NM_004791.3(ITGBL1):c.317G>A(p.Gly106Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00257 in 1,612,318 control chromosomes in the GnomAD database, including 97 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 42 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 55 hom. )
Consequence
ITGBL1
NM_004791.3 missense, splice_region
NM_004791.3 missense, splice_region
Scores
6
7
Splicing: ADA: 0.9996
2
Clinical Significance
Conservation
PhyloP100: 6.89
Publications
3 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -15 ACMG points.
PP3
Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
BP6
Variant 13-101567699-G-A is Benign according to our data. Variant chr13-101567699-G-A is described in ClinVar as [Benign]. Clinvar id is 790681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.014 (2125/152144) while in subpopulation AFR AF = 0.0481 (1996/41524). AF 95% confidence interval is 0.0463. There are 42 homozygotes in GnomAd4. There are 979 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 42 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGBL1 | NM_004791.3 | c.317G>A | p.Gly106Asp | missense_variant, splice_region_variant | Exon 3 of 11 | ENST00000376180.8 | NP_004782.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0139 AC: 2120AN: 152026Hom.: 42 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2120
AN:
152026
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00363 AC: 906AN: 249772 AF XY: 0.00255 show subpopulations
GnomAD2 exomes
AF:
AC:
906
AN:
249772
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00138 AC: 2013AN: 1460174Hom.: 55 Cov.: 30 AF XY: 0.00118 AC XY: 858AN XY: 726432 show subpopulations
GnomAD4 exome
AF:
AC:
2013
AN:
1460174
Hom.:
Cov.:
30
AF XY:
AC XY:
858
AN XY:
726432
show subpopulations
African (AFR)
AF:
AC:
1571
AN:
33352
American (AMR)
AF:
AC:
127
AN:
44584
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
26006
East Asian (EAS)
AF:
AC:
0
AN:
39650
South Asian (SAS)
AF:
AC:
5
AN:
86074
European-Finnish (FIN)
AF:
AC:
0
AN:
53384
Middle Eastern (MID)
AF:
AC:
13
AN:
5752
European-Non Finnish (NFE)
AF:
AC:
95
AN:
1111070
Other (OTH)
AF:
AC:
201
AN:
60302
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.479
Heterozygous variant carriers
0
89
178
267
356
445
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0140 AC: 2125AN: 152144Hom.: 42 Cov.: 32 AF XY: 0.0132 AC XY: 979AN XY: 74390 show subpopulations
GnomAD4 genome
AF:
AC:
2125
AN:
152144
Hom.:
Cov.:
32
AF XY:
AC XY:
979
AN XY:
74390
show subpopulations
African (AFR)
AF:
AC:
1996
AN:
41524
American (AMR)
AF:
AC:
85
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5164
South Asian (SAS)
AF:
AC:
1
AN:
4818
European-Finnish (FIN)
AF:
AC:
0
AN:
10596
Middle Eastern (MID)
AF:
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12
AN:
67990
Other (OTH)
AF:
AC:
29
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
107
215
322
430
537
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
218
ESP6500EA
AF:
AC:
1
ExAC
AF:
AC:
563
Asia WGS
AF:
AC:
13
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Jul 13, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Uncertain
D
PhyloP100
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
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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