rs150209313
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_206933.4(USH2A):c.785-16_785-15delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000534 in 1,612,814 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00081 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00051 ( 6 hom. )
Consequence
USH2A
NM_206933.4 intron
NM_206933.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.191
Genes affected
USH2A (HGNC:12601): (usherin) This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 1-216327668-CAT-C is Benign according to our data. Variant chr1-216327668-CAT-C is described in ClinVar as [Benign]. Clinvar id is 227147.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-216327668-CAT-C is described in Lovd as [Benign]. Variant chr1-216327668-CAT-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000808 (123/152238) while in subpopulation EAS AF= 0.0209 (108/5174). AF 95% confidence interval is 0.0177. There are 2 homozygotes in gnomad4. There are 58 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.785-16_785-15delAT | intron_variant | ENST00000307340.8 | NP_996816.3 | |||
USH2A | NM_007123.6 | c.785-16_785-15delAT | intron_variant | NP_009054.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.785-16_785-15delAT | intron_variant | 1 | NM_206933.4 | ENSP00000305941.3 | ||||
USH2A | ENST00000366942.3 | c.785-16_785-15delAT | intron_variant | 1 | ENSP00000355909.3 | |||||
USH2A | ENST00000674083.1 | c.785-16_785-15delAT | intron_variant | ENSP00000501296.1 |
Frequencies
GnomAD3 genomes AF: 0.000815 AC: 124AN: 152120Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00131 AC: 329AN: 250668Hom.: 3 AF XY: 0.00123 AC XY: 167AN XY: 135484
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GnomAD4 exome AF: 0.000505 AC: 738AN: 1460576Hom.: 6 AF XY: 0.000519 AC XY: 377AN XY: 726604
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GnomAD4 genome AF: 0.000808 AC: 123AN: 152238Hom.: 2 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 05, 2015 | c.785-16_785-15delAT in intron 4 of USH2A: This variant is not expected to have clinical significance because it has been identified in 1.6% (134/8536) of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadin stitute.org; dbSNP rs150209313). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Retinitis pigmentosa 39 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Usher syndrome type 2A Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at