17-47253904-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS1
The NM_000212.3(ITGB3):c.43C>T(p.Leu15Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,396,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
ITGB3
NM_000212.3 synonymous
NM_000212.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.08
Genes affected
ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
Variant 17-47253904-C-T is Benign according to our data. Variant chr17-47253904-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3606260.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.09 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.0000217 (27/1244656) while in subpopulation EAS AF= 0.000984 (27/27440). AF 95% confidence interval is 0.000694. There are 0 homozygotes in gnomad4_exome. There are 15 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGB3 | ENST00000559488.7 | c.43C>T | p.Leu15Leu | synonymous_variant | 1/15 | 1 | NM_000212.3 | ENSP00000452786.2 | ||
ITGB3 | ENST00000571680.1 | c.43C>T | p.Leu15Leu | synonymous_variant | 1/9 | 1 | ENSP00000461626.1 | |||
ENSG00000259753 | ENST00000560629.1 | n.7C>T | non_coding_transcript_exon_variant | 1/18 | 2 | ENSP00000456711.2 | ||||
ITGB3 | ENST00000696963.1 | c.43C>T | p.Leu15Leu | synonymous_variant | 1/14 | ENSP00000513002.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151818Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000217 AC: 27AN: 1244656Hom.: 0 Cov.: 30 AF XY: 0.0000245 AC XY: 15AN XY: 611804
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151926Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at