chr11-83166528-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001346413.3(PCF11):c.1631C>T(p.Ala544Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,634 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001346413.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCF11 | NM_001346413.3 | c.1631C>T | p.Ala544Val | missense_variant | 5/16 | ENST00000690938.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCF11 | ENST00000690938.1 | c.1631C>T | p.Ala544Val | missense_variant | 5/16 | NM_001346413.3 | P3 | ||
PCF11 | ENST00000298281.8 | c.1631C>T | p.Ala544Val | missense_variant | 5/16 | 1 | A1 | ||
PCF11 | ENST00000530304.5 | c.1631C>T | p.Ala544Val | missense_variant | 5/8 | 1 | |||
PCF11 | ENST00000530660.5 | c.1631C>T | p.Ala544Val | missense_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152042Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248918Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135046
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461592Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727084
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.1631C>T (p.A544V) alteration is located in exon 5 (coding exon 5) of the PCF11 gene. This alteration results from a C to T substitution at nucleotide position 1631, causing the alanine (A) at amino acid position 544 to be replaced by a valine (V). 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