chr1-99689249-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017734.5(PALMD):c.989G>A(p.Arg330Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,498 control chromosomes in the GnomAD database, including 1 homozygotes. 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_017734.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALMD | NM_017734.5 | c.989G>A | p.Arg330Gln | missense_variant | 7/8 | ENST00000263174.9 | NP_060204.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALMD | ENST00000263174.9 | c.989G>A | p.Arg330Gln | missense_variant | 7/8 | 1 | NM_017734.5 | ENSP00000263174.4 | ||
PALMD | ENST00000605497.5 | c.989G>A | p.Arg330Gln | missense_variant | 7/7 | 1 | ENSP00000473839.1 | |||
PALMD | ENST00000496843.1 | n.4148G>A | non_coding_transcript_exon_variant | 4/5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151806Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 250146Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135168
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461574Hom.: 1 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727086
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151924Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.989G>A (p.R330Q) alteration is located in exon 7 (coding exon 7) of the PALMD gene. This alteration results from a G to A substitution at nucleotide position 989, causing the arginine (R) at amino acid position 330 to be replaced by a glutamine (Q). 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