2-27137339-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178553.4(PRR30):c.991T>G(p.Cys331Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000743 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178553.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR30 | NM_178553.4 | c.991T>G | p.Cys331Gly | missense_variant | 3/3 | ENST00000335524.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR30 | ENST00000335524.7 | c.991T>G | p.Cys331Gly | missense_variant | 3/3 | 1 | NM_178553.4 | P1 | |
PRR30 | ENST00000432962.2 | c.497T>G | p.Leu166Arg | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251388Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135892
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461860Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 49AN XY: 727238
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2022 | The c.991T>G (p.C331G) alteration is located in exon 3 (coding exon 1) of the PRR30 gene. This alteration results from a T to G substitution at nucleotide position 991, causing the cysteine (C) at amino acid position 331 to be replaced by a glycine (G). 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