chr17-75754778-C-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_000213.5(ITGB4):āc.4521C>Gā(p.Pro1507=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,613,648 control chromosomes in the GnomAD database, including 182,550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P1507P) has been classified as Likely benign.
Frequency
Consequence
NM_000213.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB4 | NM_000213.5 | c.4521C>G | p.Pro1507= | synonymous_variant | 34/40 | ENST00000200181.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB4 | ENST00000200181.8 | c.4521C>G | p.Pro1507= | synonymous_variant | 34/40 | 1 | NM_000213.5 |
Frequencies
GnomAD3 genomes AF: 0.385 AC: 58544AN: 151918Hom.: 13135 Cov.: 32
GnomAD3 exomes AF: 0.455 AC: 114338AN: 251118Hom.: 27133 AF XY: 0.460 AC XY: 62505AN XY: 135746
GnomAD4 exome AF: 0.477 AC: 696779AN: 1461612Hom.: 169418 Cov.: 55 AF XY: 0.476 AC XY: 346136AN XY: 727118
GnomAD4 genome AF: 0.385 AC: 58538AN: 152036Hom.: 13132 Cov.: 32 AF XY: 0.389 AC XY: 28927AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Junctional epidermolysis bullosa with pyloric atresia Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Junctional epidermolysis bullosa, non-Herlitz type Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Epidermolysis bullosa simplex 1C, localized Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Deficiency of galactokinase Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at