chr3-37508677-T-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002207.3(ITGA9):c.897+50T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000681 in 1,484,606 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00079 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00067 ( 11 hom. )
Consequence
ITGA9
NM_002207.3 intron
NM_002207.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.762
Genes affected
ITGA9 (HGNC:6145): (integrin subunit alpha 9) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane glycoproteins composed of an alpha chain and a beta chain that mediate cell-cell and cell-matrix adhesion. The protein encoded by this gene, when bound to the beta 1 chain, forms an integrin that is a receptor for VCAM1, cytotactin and osteopontin. Expression of this gene has been found to be upregulated in small cell lung cancers. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 3-37508677-T-A is Benign according to our data. Variant chr3-37508677-T-A is described in ClinVar as [Benign]. Clinvar id is 496844.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000794 (121/152324) while in subpopulation EAS AF= 0.0221 (115/5192). AF 95% confidence interval is 0.0189. There are 1 homozygotes in gnomad4. There are 70 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 11 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGA9 | NM_002207.3 | c.897+50T>A | intron_variant | ENST00000264741.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGA9 | ENST00000264741.10 | c.897+50T>A | intron_variant | 1 | NM_002207.3 | P1 | |||
ITGA9 | ENST00000422441.5 | c.897+50T>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152206Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00204 AC: 507AN: 248748Hom.: 11 AF XY: 0.00185 AC XY: 249AN XY: 134576
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GnomAD4 exome AF: 0.000668 AC: 890AN: 1332282Hom.: 11 Cov.: 20 AF XY: 0.000637 AC XY: 427AN XY: 670444
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GnomAD4 genome AF: 0.000794 AC: 121AN: 152324Hom.: 1 Cov.: 32 AF XY: 0.000940 AC XY: 70AN XY: 74492
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 09, 2017 | - - |
Computational 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