chr6-31624444-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004638.4(PRRC2A):c.391-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,460,652 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004638.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.391-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000376033.3 | |||
PRRC2A | NM_080686.3 | c.391-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
PRRC2A | XM_047419336.1 | c.391-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.391-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004638.4 | P1 | |||
PRRC2A | ENST00000376007.8 | c.391-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
ENST00000687518.1 | c.137-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | P1 | ||||||
PRRC2A | ENST00000469577.5 | n.236-6C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251438Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135912
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460652Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 726730
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
PRRC2A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 2019 | 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