chr12-41188727-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164595.2(PDZRN4):c.272C>T(p.Ser91Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000585 in 1,554,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001164595.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZRN4 | NM_001164595.2 | c.272C>T | p.Ser91Leu | missense_variant | 1/10 | ENST00000402685.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN4 | ENST00000402685.7 | c.272C>T | p.Ser91Leu | missense_variant | 1/10 | 2 | NM_001164595.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152020Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000483 AC: 8AN: 165666Hom.: 0 AF XY: 0.0000539 AC XY: 5AN XY: 92736
GnomAD4 exome AF: 0.0000606 AC: 85AN: 1402350Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 44AN XY: 694950
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | The c.272C>T (p.S91L) alteration is located in exon 1 (coding exon 1) of the PDZRN4 gene. This alteration results from a C to T substitution at nucleotide position 272, causing the serine (S) at amino acid position 91 to be replaced by a leucine (L). 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