chr19-14053615-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001145028.2(PALM3):c.2057C>T(p.Ala686Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000241 in 1,456,422 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145028.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALM3 | NM_001145028.2 | c.2057C>T | p.Ala686Val | missense_variant | 7/7 | ENST00000669674.2 | NP_001138500.2 | |
PALM3 | NM_001367327.1 | c.1859C>T | p.Ala620Val | missense_variant | 5/5 | NP_001354256.1 | ||
PALM3 | XM_047438763.1 | c.1976C>T | p.Ala659Val | missense_variant | 6/6 | XP_047294719.1 | ||
PALM3 | XM_047438764.1 | c.1859C>T | p.Ala620Val | missense_variant | 5/5 | XP_047294720.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALM3 | ENST00000669674.2 | c.2057C>T | p.Ala686Val | missense_variant | 7/7 | NM_001145028.2 | ENSP00000499271.1 | |||
PALM3 | ENST00000340790.9 | c.2012C>T | p.Ala671Val | missense_variant | 6/6 | 5 | ENSP00000344996.3 | |||
PALM3 | ENST00000661591.1 | c.1937C>T | p.Ala646Val | missense_variant | 4/4 | ENSP00000499248.1 | ||||
PALM3 | ENST00000589048.2 | c.1859C>T | p.Ala620Val | missense_variant | 5/5 | 3 | ENSP00000465701.2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000389 AC: 31AN: 79642Hom.: 0 AF XY: 0.000439 AC XY: 17AN XY: 38726
GnomAD4 exome AF: 0.000249 AC: 325AN: 1304146Hom.: 2 Cov.: 30 AF XY: 0.000289 AC XY: 183AN XY: 632860
GnomAD4 genome AF: 0.000171 AC: 26AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.2012C>T (p.A671V) alteration is located in exon 6 (coding exon 6) of the PALM3 gene. This alteration results from a C to T substitution at nucleotide position 2012, causing the alanine (A) at amino acid position 671 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