chr11-35435924-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001001991.3(PAMR1):c.1312C>T(p.Arg438Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,722 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R438Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001001991.3 missense
Scores
Clinical Significance
Conservation
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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.1312C>T | p.Arg438Trp | missense_variant | 9/11 | ENST00000619888.5 | |
PAMR1 | NM_015430.4 | c.1363C>T | p.Arg455Trp | missense_variant | 10/12 | ||
PAMR1 | NM_001282675.2 | c.1192C>T | p.Arg398Trp | missense_variant | 11/13 | ||
PAMR1 | NM_001282676.2 | c.979C>T | p.Arg327Trp | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAMR1 | ENST00000619888.5 | c.1312C>T | p.Arg438Trp | missense_variant | 9/11 | 1 | NM_001001991.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251322Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135812
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461462Hom.: 1 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727090
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2022 | The c.1363C>T (p.R455W) alteration is located in exon 10 (coding exon 10) of the PAMR1 gene. This alteration results from a C to T substitution at nucleotide position 1363, causing the arginine (R) at amino acid position 455 to be replaced by a tryptophan (W). 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