rs1187075
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002211.4(ITGB1):c.-1+277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,990 control chromosomes in the GnomAD database, including 53,166 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.83 ( 53130 hom., cov: 33)
Exomes 𝑓: 0.88 ( 36 hom. )
Consequence
ITGB1
NM_002211.4 intron
NM_002211.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.26
Genes affected
ITGB1 (HGNC:6153): (integrin subunit beta 1) Integrins are heterodimeric proteins made up of alpha and beta subunits. At least 18 alpha and 8 beta subunits have been described in mammals. Integrin family members are membrane receptors involved in cell adhesion and recognition in a variety of processes including embryogenesis, hemostasis, tissue repair, immune response and metastatic diffusion of tumor cells. This gene encodes a beta subunit. Multiple alternatively spliced transcript variants which encode different protein isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.-1+277T>C | intron_variant | ENST00000302278.8 | |||
ITGB1 | NM_133376.3 | c.-110T>C | 5_prime_UTR_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB1 | ENST00000302278.8 | c.-1+277T>C | intron_variant | 1 | NM_002211.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.831 AC: 126149AN: 151788Hom.: 53094 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
126149
AN:
151788
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.880 AC: 81AN: 92Hom.: 36 Cov.: 0 AF XY: 0.897 AC XY: 61AN XY: 68
GnomAD4 exome
AF:
AC:
81
AN:
92
Hom.:
Cov.:
0
AF XY:
AC XY:
61
AN XY:
68
Gnomad4 AFR exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.831 AC: 126234AN: 151898Hom.: 53130 Cov.: 33 AF XY: 0.831 AC XY: 61675AN XY: 74252
GnomAD4 genome
?
AF:
AC:
126234
AN:
151898
Hom.:
Cov.:
33
AF XY:
AC XY:
61675
AN XY:
74252
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2835
AN:
3442
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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