chr10-47348472-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002900.3(RBP3):c.-13C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 1,599,754 control chromosomes in the GnomAD database, including 6,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002900.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0736 AC: 11198AN: 152076Hom.: 555 Cov.: 33
GnomAD3 exomes AF: 0.0982 AC: 23267AN: 237010Hom.: 1436 AF XY: 0.101 AC XY: 13139AN XY: 129640
GnomAD4 exome AF: 0.0846 AC: 122414AN: 1447560Hom.: 5964 Cov.: 32 AF XY: 0.0870 AC XY: 62679AN XY: 720446
GnomAD4 genome AF: 0.0736 AC: 11203AN: 152194Hom.: 557 Cov.: 33 AF XY: 0.0750 AC XY: 5580AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:1
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Retinitis pigmentosa Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Retinitis pigmentosa 66 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at