chr19-44650064-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006505.5(PVR):c.683T>C(p.Phe228Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000903 in 1,550,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006505.5 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 |
---|---|---|---|---|---|---|---|
PVR | NM_006505.5 | c.683T>C | p.Phe228Ser | missense_variant | 3/8 | ENST00000425690.8 | |
PVR | NM_001135770.4 | c.683T>C | p.Phe228Ser | missense_variant | 3/6 | ||
PVR | NM_001135768.3 | c.683T>C | p.Phe228Ser | missense_variant | 3/8 | ||
PVR | NM_001135769.3 | c.683T>C | p.Phe228Ser | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PVR | ENST00000425690.8 | c.683T>C | p.Phe228Ser | missense_variant | 3/8 | 1 | NM_006505.5 | P2 | |
CEACAM16-AS1 | ENST00000662585.1 | n.476-17445A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000404 AC: 8AN: 198054Hom.: 0 AF XY: 0.0000381 AC XY: 4AN XY: 105076
GnomAD4 exome AF: 0.00000644 AC: 9AN: 1398548Hom.: 0 Cov.: 31 AF XY: 0.00000726 AC XY: 5AN XY: 688584
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.683T>C (p.F228S) alteration is located in exon 3 (coding exon 3) of the PVR gene. This alteration results from a T to C substitution at nucleotide position 683, causing the phenylalanine (F) at amino acid position 228 to be replaced by a serine (S). 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