17-50072022-C-T
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_002204.4(ITGA3):c.996C>T(p.Phe332=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,613,448 control chromosomes in the GnomAD database, including 16,649 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 3528 hom., cov: 31)
Exomes 𝑓: 0.11 ( 13121 hom. )
Consequence
ITGA3
NM_002204.4 synonymous
NM_002204.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.999
Genes affected
ITGA3 (HGNC:6139): (integrin subunit alpha 3) The gene encodes a member of the integrin alpha chain family of proteins. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain that function as cell surface adhesion molecules. The encoded preproprotein is proteolytically processed to generate light and heavy chains that comprise the alpha 3 subunit. This subunit joins with a beta 1 subunit to form an integrin that interacts with extracellular matrix proteins including members of the laminin family. Expression of this gene may be correlated with breast cancer metastasis. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 17-50072022-C-T is Benign according to our data. Variant chr17-50072022-C-T is described in ClinVar as [Benign]. Clinvar id is 1271410.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.999 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGA3 | NM_002204.4 | c.996C>T | p.Phe332= | synonymous_variant | 7/26 | ENST00000320031.13 | NP_002195.1 | |
ITGA3 | XM_047435922.1 | c.996C>T | p.Phe332= | synonymous_variant | 7/18 | XP_047291878.1 | ||
ITGA3 | XM_005257308.3 | c.751+1092C>T | intron_variant | XP_005257365.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITGA3 | ENST00000320031.13 | c.996C>T | p.Phe332= | synonymous_variant | 7/26 | 1 | NM_002204.4 | ENSP00000315190 | P1 |
Frequencies
GnomAD3 genomes AF: 0.185 AC: 28077AN: 151844Hom.: 3511 Cov.: 31
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GnomAD3 exomes AF: 0.167 AC: 41908AN: 250798Hom.: 4639 AF XY: 0.162 AC XY: 21919AN XY: 135622
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GnomAD4 exome AF: 0.114 AC: 166596AN: 1461486Hom.: 13121 Cov.: 33 AF XY: 0.116 AC XY: 84575AN XY: 727078
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GnomAD4 genome AF: 0.185 AC: 28157AN: 151962Hom.: 3528 Cov.: 31 AF XY: 0.189 AC XY: 14048AN XY: 74274
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
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CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at