chr2-29061940-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001029883.3(PCARE):c.*2929T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,246 control chromosomes in the GnomAD database, including 67,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.94 ( 67351 hom., cov: 32)
Exomes 𝑓: 1.0 ( 9 hom. )
Consequence
PCARE
NM_001029883.3 3_prime_UTR
NM_001029883.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.498
Genes affected
PCARE (HGNC:34383): (photoreceptor cilium actin regulator) The protein encoded by this gene is highly expressed in photoreceptors and may associate with the primary cilium of the outer segment. The encoded protein appears to undergo post-translational lipid modification. Nonsense and missense variants of this gene appear to cause a recessive form of retinitis pigmentosa. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 2-29061940-A-G is Benign according to our data. Variant chr2-29061940-A-G is described in ClinVar as [Benign]. Clinvar id is 335573.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCARE | NM_001029883.3 | c.*2929T>C | 3_prime_UTR_variant | 2/2 | ENST00000331664.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCARE | ENST00000331664.6 | c.*2929T>C | 3_prime_UTR_variant | 2/2 | 2 | NM_001029883.3 | P1 | ||
PCARE | ENST00000602958.1 | n.216T>C | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.936 AC: 142308AN: 152110Hom.: 67326 Cov.: 32
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GnomAD4 exome AF: 1.00 AC: 18AN: 18Hom.: 9 Cov.: 0 AF XY: 1.00 AC XY: 6AN XY: 6
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GnomAD4 genome AF: 0.935 AC: 142386AN: 152228Hom.: 67351 Cov.: 32 AF XY: 0.937 AC XY: 69761AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinitis pigmentosa Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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