chr15-90969493-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003981.4(PRC1):c.1703G>A(p.Arg568His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,611,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003981.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRC1 | NM_003981.4 | c.1703G>A | p.Arg568His | missense_variant | 13/15 | ENST00000394249.8 | |
PRC1-AS1 | NR_051984.1 | n.310+2815C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRC1 | ENST00000394249.8 | c.1703G>A | p.Arg568His | missense_variant | 13/15 | 1 | NM_003981.4 | ||
PRC1-AS1 | ENST00000554388.2 | n.339+2815C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248874Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134516
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1458946Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725838
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2022 | The c.1703G>A (p.R568H) alteration is located in exon 13 (coding exon 13) of the PRC1 gene. This alteration results from a G to A substitution at nucleotide position 1703, causing the arginine (R) at amino acid position 568 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at