rs747065891
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_206933.4(USH2A):c.5130C>T(p.Pro1710Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_206933.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USH2A | NM_206933.4 | c.5130C>T | p.Pro1710Pro | synonymous_variant | Exon 25 of 72 | ENST00000307340.8 | NP_996816.3 | |
USH2A-AS2 | NR_125992.1 | n.266-1987G>A | intron_variant | Intron 2 of 2 | ||||
USH2A-AS2 | NR_125993.1 | n.137-1987G>A | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250524Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135360
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461148Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726876
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74248
ClinVar
Submissions by phenotype
not specified Benign:1
p.Pro1710Pro in exon 25 of USH2A: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. It has been identified in 3/121051 chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs747065891). -
not provided Benign:1
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Retinitis pigmentosa 39 Benign:1
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Usher syndrome type 2A Benign:1
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USH2A-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at