chr9-131436625-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013318.4(PRRC2B):āc.299G>Cā(p.Ser100Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_013318.4 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 |
---|---|---|---|---|---|---|---|
PRRC2B | NM_013318.4 | c.299G>C | p.Ser100Thr | missense_variant | 4/32 | ENST00000683519.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2B | ENST00000683519.1 | c.299G>C | p.Ser100Thr | missense_variant | 4/32 | NM_013318.4 | P2 | ||
ENST00000691540.1 | c.42G>C | p.Gln14His | missense_variant | 2/5 | P1 | ||||
PRRC2B | ENST00000684596.1 | c.299G>C | p.Ser100Thr | missense_variant | 4/32 | P2 | |||
PRRC2B | ENST00000682501.1 | c.299G>C | p.Ser100Thr | missense_variant | 4/31 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248516Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134858
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461090Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726836
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.299G>C (p.S100T) alteration is located in exon 3 (coding exon 3) of the PRRC2B gene. This alteration results from a G to C substitution at nucleotide position 299, causing the serine (S) at amino acid position 100 to be replaced by a threonine (T). 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