rs7116432
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000428726.8(CD44):c.2024+779A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,097,788 control chromosomes in the GnomAD database, including 71,016 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.35 ( 10262 hom., cov: 29)
Exomes 𝑓: 0.35 ( 60754 hom. )
Consequence
CD44
ENST00000428726.8 intron
ENST00000428726.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.322
Genes affected
CD44 (HGNC:1681): (CD44 molecule (IN blood group)) The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD44 | NM_000610.4 | c.2024+779A>G | intron_variant | ENST00000428726.8 | NP_000601.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD44 | ENST00000428726.8 | c.2024+779A>G | intron_variant | 1 | NM_000610.4 | ENSP00000398632 | A2 |
Frequencies
GnomAD3 genomes AF: 0.349 AC: 52685AN: 151064Hom.: 10267 Cov.: 29
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GnomAD4 exome AF: 0.351 AC: 332511AN: 946626Hom.: 60754 Cov.: 19 AF XY: 0.355 AC XY: 160490AN XY: 452076
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GnomAD4 genome AF: 0.349 AC: 52685AN: 151162Hom.: 10262 Cov.: 29 AF XY: 0.359 AC XY: 26519AN XY: 73834
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Calcium oxalate urolithiasis Other:1
association, no assertion criteria provided | case-control | Division of Molecular Genetics and Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University | Mar 01, 2014 | - - |
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