11-35432808-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001001991.3(PAMR1):c.1711C>T(p.Arg571Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000311 in 1,607,768 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R571H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001991.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAMR1 | NM_001001991.3 | c.1711C>T | p.Arg571Cys | missense_variant | 11/11 | ENST00000619888.5 | |
PAMR1 | NM_015430.4 | c.1762C>T | p.Arg588Cys | missense_variant | 12/12 | ||
PAMR1 | NM_001282675.2 | c.1591C>T | p.Arg531Cys | missense_variant | 13/13 | ||
PAMR1 | NM_001282676.2 | c.1378C>T | p.Arg460Cys | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAMR1 | ENST00000619888.5 | c.1711C>T | p.Arg571Cys | missense_variant | 11/11 | 1 | NM_001001991.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000528 AC: 13AN: 246068Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133312
GnomAD4 exome AF: 0.0000220 AC: 32AN: 1455432Hom.: 0 Cov.: 32 AF XY: 0.0000166 AC XY: 12AN XY: 724200
GnomAD4 genome AF: 0.000118 AC: 18AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.1762C>T (p.R588C) alteration is located in exon 12 (coding exon 12) of the PAMR1 gene. This alteration results from a C to T substitution at nucleotide position 1762, causing the arginine (R) at amino acid position 588 to be replaced by a cysteine (C). 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