rs11574541
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_000889.3(ITGB7):c.1788C>T(p.Cys596=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00052 in 1,614,146 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0019 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 7 hom. )
Consequence
ITGB7
NM_000889.3 synonymous
NM_000889.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.47
Genes affected
ITGB7 (HGNC:6162): (integrin subunit beta 7) This gene encodes a protein that is a member of the integrin superfamily. Members of this family are adhesion receptors that function in signaling from the extracellular matrix to the cell. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. The encoded protein forms dimers with an alpha4 chain or an alphaE chain and plays a role in leukocyte adhesion. Dimerization with alpha4 forms a homing receptor for migration of lymphocytes to the intestinal mucosa and Peyer's patches. Dimerization with alphaE permits binding to the ligand epithelial cadherin, a calcium-dependent adhesion molecule. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]
ZNF740 (HGNC:27465): (zinc finger protein 740) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP7
?
Synonymous conserved (PhyloP=-1.47 with no splicing effect.
BS2
?
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGB7 | NM_000889.3 | c.1788C>T | p.Cys596= | synonymous_variant | 13/16 | ENST00000267082.10 | |
ZNF740 | NM_001004304.4 | c.*5259G>A | 3_prime_UTR_variant | 7/7 | ENST00000416904.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGB7 | ENST00000267082.10 | c.1788C>T | p.Cys596= | synonymous_variant | 13/16 | 1 | NM_000889.3 | P1 | |
ZNF740 | ENST00000416904.5 | c.*5259G>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001004304.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 288AN: 152166Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.00118 AC: 295AN: 250276Hom.: 3 AF XY: 0.00103 AC XY: 139AN XY: 135334
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GnomAD4 exome AF: 0.000378 AC: 552AN: 1461862Hom.: 7 Cov.: 32 AF XY: 0.000352 AC XY: 256AN XY: 727228
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GnomAD4 genome ? AF: 0.00189 AC: 288AN: 152284Hom.: 5 Cov.: 32 AF XY: 0.00184 AC XY: 137AN XY: 74466
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at