19-43487051-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_198850.4(PHLDB3):c.1222C>T(p.Pro408Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000429 in 1,579,144 control chromosomes in the GnomAD database, including 1 homozygotes. 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_198850.4 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 |
---|---|---|---|---|---|---|---|
PHLDB3 | NM_198850.4 | c.1222C>T | p.Pro408Ser | missense_variant | 10/16 | ENST00000292140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHLDB3 | ENST00000292140.10 | c.1222C>T | p.Pro408Ser | missense_variant | 10/16 | 5 | NM_198850.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000217 AC: 43AN: 198190Hom.: 0 AF XY: 0.000187 AC XY: 20AN XY: 106742
GnomAD4 exome AF: 0.000449 AC: 640AN: 1426896Hom.: 1 Cov.: 32 AF XY: 0.000444 AC XY: 314AN XY: 707196
GnomAD4 genome AF: 0.000250 AC: 38AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1222C>T (p.P408S) alteration is located in exon 10 (coding exon 9) of the PHLDB3 gene. This alteration results from a C to T substitution at nucleotide position 1222, causing the proline (P) at amino acid position 408 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