11-83166608-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001346413.3(PCF11):c.1711A>T(p.Asn571Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,461,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001346413.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCF11 | NM_001346413.3 | c.1711A>T | p.Asn571Tyr | missense_variant | 5/16 | ENST00000690938.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCF11 | ENST00000690938.1 | c.1711A>T | p.Asn571Tyr | missense_variant | 5/16 | NM_001346413.3 | P3 | ||
PCF11 | ENST00000298281.8 | c.1711A>T | p.Asn571Tyr | missense_variant | 5/16 | 1 | A1 | ||
PCF11 | ENST00000530304.5 | c.1711A>T | p.Asn571Tyr | missense_variant | 5/8 | 1 | |||
PCF11 | ENST00000530660.5 | c.1711A>T | p.Asn571Tyr | missense_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248070Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134780
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461606Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 727090
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1711A>T (p.N571Y) alteration is located in exon 5 (coding exon 5) of the PCF11 gene. This alteration results from a A to T substitution at nucleotide position 1711, causing the asparagine (N) at amino acid position 571 to be replaced by a tyrosine (Y). 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