chr17-75752241-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000213.5(ITGB4):c.3861C>T(p.Asn1287Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,613,712 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 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITGB4 | NM_000213.5 | c.3861C>T | p.Asn1287Asn | synonymous_variant | Exon 31 of 40 | ENST00000200181.8 | NP_000204.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 351AN: 152246Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00195 AC: 490AN: 251278Hom.: 3 AF XY: 0.00194 AC XY: 264AN XY: 135872
GnomAD4 exome AF: 0.00353 AC: 5165AN: 1461348Hom.: 10 Cov.: 33 AF XY: 0.00347 AC XY: 2521AN XY: 726974
GnomAD4 genome AF: 0.00230 AC: 351AN: 152364Hom.: 2 Cov.: 33 AF XY: 0.00197 AC XY: 147AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:6
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ITGB4: BP4, BS2 -
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Junctional epidermolysis bullosa with pyloric atresia Benign:1
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at