17-17206019-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_178836.4(PLD6):c.268G>C(p.Ala90Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000778 in 1,542,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178836.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLD6 | ENST00000321560.4 | c.268G>C | p.Ala90Pro | missense_variant | Exon 1 of 2 | 1 | NM_178836.4 | ENSP00000317177.3 | ||
ENSG00000264187 | ENST00000427497.3 | n.*417+1006G>C | intron_variant | Intron 10 of 11 | 1 | ENSP00000394249.3 | ||||
MPRIP | ENST00000578209.5 | c.*17+4386C>G | intron_variant | Intron 5 of 5 | 3 | ENSP00000464276.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000962 AC: 13AN: 135130Hom.: 0 AF XY: 0.000108 AC XY: 8AN XY: 74150
GnomAD4 exome AF: 0.00000647 AC: 9AN: 1390680Hom.: 0 Cov.: 32 AF XY: 0.00000728 AC XY: 5AN XY: 686612
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.268G>C (p.A90P) alteration is located in exon 1 (coding exon 1) of the PLD6 gene. This alteration results from a G to C substitution at nucleotide position 268, causing the alanine (A) at amino acid position 90 to be replaced by a proline (P). 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