10-71712675-T-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_022124.6(CDH23):āc.3231T>Gā(p.Pro1077=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,613,460 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00014 ( 0 hom., cov: 33)
Exomes š: 0.000095 ( 1 hom. )
Consequence
CDH23
NM_022124.6 synonymous
NM_022124.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.19
Genes affected
CDH23 (HGNC:13733): (cadherin related 23) This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 10-71712675-T-G is Benign according to our data. Variant chr10-71712675-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 681868.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.18 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH23 | NM_022124.6 | c.3231T>G | p.Pro1077= | synonymous_variant | 28/70 | ENST00000224721.12 | |
C10orf105 | NM_001164375.3 | c.*3261A>C | 3_prime_UTR_variant | 2/2 | ENST00000441508.4 | ||
CDH23 | NM_001171930.2 | c.3231T>G | p.Pro1077= | synonymous_variant | 28/32 | ||
C10orf105 | NM_001168390.2 | c.*3261A>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH23 | ENST00000224721.12 | c.3231T>G | p.Pro1077= | synonymous_variant | 28/70 | 5 | NM_022124.6 | P1 | |
C10orf105 | ENST00000441508.4 | c.*3261A>C | 3_prime_UTR_variant | 2/2 | 1 | NM_001164375.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152210Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000129 AC: 32AN: 248538Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 135064
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GnomAD4 exome AF: 0.0000951 AC: 139AN: 1461250Hom.: 1 Cov.: 31 AF XY: 0.0000991 AC XY: 72AN XY: 726898
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GnomAD4 genome AF: 0.000145 AC: 22AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | CDH23: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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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