1-215625538-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_206933.4(USH2A):c.*243G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0085 in 543,290 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 105 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 34 hom. )
Consequence
USH2A
NM_206933.4 3_prime_UTR
NM_206933.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.335
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 1-215625538-C-A is Benign according to our data. Variant chr1-215625538-C-A is described in ClinVar as [Benign]. Clinvar id is 1297792.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0712 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.*243G>T | 3_prime_UTR_variant | 72/72 | ENST00000307340.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USH2A | ENST00000307340.8 | c.*243G>T | 3_prime_UTR_variant | 72/72 | 1 | NM_206933.4 | P1 | ||
USH2A | ENST00000674083.1 | c.*243G>T | 3_prime_UTR_variant | 73/73 |
Frequencies
GnomAD3 genomes ? AF: 0.0216 AC: 3292AN: 152112Hom.: 105 Cov.: 32
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GnomAD4 exome AF: 0.00338 AC: 1323AN: 391060Hom.: 34 Cov.: 3 AF XY: 0.00283 AC XY: 589AN XY: 208236
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GnomAD4 genome ? AF: 0.0217 AC: 3297AN: 152230Hom.: 105 Cov.: 32 AF XY: 0.0197 AC XY: 1464AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at