chr10-32911570-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002211.4(ITGB1):c.1809C>T(p.Asn603=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,614,116 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 21 hom., cov: 32)
Exomes 𝑓: 0.00077 ( 13 hom. )
Consequence
ITGB1
NM_002211.4 synonymous
NM_002211.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.225
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 10-32911570-G-A is Benign according to our data. Variant chr10-32911570-G-A is described in ClinVar as [Benign]. Clinvar id is 712042.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.225 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00782 (1190/152252) while in subpopulation AFR AF= 0.0264 (1097/41536). AF 95% confidence interval is 0.0251. There are 21 homozygotes in gnomad4. There are 588 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1188 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB1 | NM_002211.4 | c.1809C>T | p.Asn603= | synonymous_variant | 13/16 | ENST00000302278.8 | |
ITGB1 | NM_033668.2 | c.1809C>T | p.Asn603= | synonymous_variant | 12/16 | ||
ITGB1 | NM_133376.3 | c.1809C>T | p.Asn603= | synonymous_variant | 13/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB1 | ENST00000302278.8 | c.1809C>T | p.Asn603= | synonymous_variant | 13/16 | 1 | NM_002211.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00781 AC: 1188AN: 152134Hom.: 20 Cov.: 32
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GnomAD3 exomes AF: 0.00194 AC: 489AN: 251428Hom.: 7 AF XY: 0.00153 AC XY: 208AN XY: 135890
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GnomAD4 exome AF: 0.000766 AC: 1120AN: 1461864Hom.: 13 Cov.: 32 AF XY: 0.000682 AC XY: 496AN XY: 727230
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GnomAD4 genome ? AF: 0.00782 AC: 1190AN: 152252Hom.: 21 Cov.: 32 AF XY: 0.00790 AC XY: 588AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at