chr17-4810949-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002663.5(PLD2):c.1008G>A(p.Arg336=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000995 in 1,608,582 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002663.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD2 | NM_002663.5 | c.1008G>A | p.Arg336= | splice_region_variant, synonymous_variant | 10/25 | ENST00000263088.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD2 | ENST00000263088.11 | c.1008G>A | p.Arg336= | splice_region_variant, synonymous_variant | 10/25 | 1 | NM_002663.5 | P1 | |
PLD2 | ENST00000572940.5 | c.1008G>A | p.Arg336= | splice_region_variant, synonymous_variant | 10/25 | 1 | |||
PLD2 | ENST00000575813.5 | c.144G>A | p.Arg48= | splice_region_variant, synonymous_variant, NMD_transcript_variant | 1/4 | 4 | |||
PLD2 | ENST00000575246.6 | c.*656G>A | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 10/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000624 AC: 95AN: 152168Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000595 AC: 146AN: 245242Hom.: 0 AF XY: 0.000655 AC XY: 87AN XY: 132782
GnomAD4 exome AF: 0.00103 AC: 1505AN: 1456414Hom.: 1 Cov.: 31 AF XY: 0.00103 AC XY: 745AN XY: 724502
GnomAD4 genome AF: 0.000624 AC: 95AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.000700 AC XY: 52AN XY: 74338
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at