chr3-37508677-T-A
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 GnomAdExome 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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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