14-104928936-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_138790.5(PLD4):c.468+4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000598 in 1,590,982 control chromosomes in the GnomAD database, including 10 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_138790.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLD4 | NM_138790.5 | c.468+4C>T | splice_region_variant, intron_variant | Intron 4 of 10 | ENST00000392593.9 | NP_620145.2 | ||
PLD4 | NM_001308174.2 | c.489+4C>T | splice_region_variant, intron_variant | Intron 4 of 10 | NP_001295103.1 | |||
PLD4 | XM_011536411.3 | c.489+4C>T | splice_region_variant, intron_variant | Intron 4 of 10 | XP_011534713.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152170Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000967 AC: 234AN: 242018Hom.: 4 AF XY: 0.00123 AC XY: 162AN XY: 131732
GnomAD4 exome AF: 0.000628 AC: 903AN: 1438694Hom.: 10 Cov.: 31 AF XY: 0.000869 AC XY: 618AN XY: 711194
GnomAD4 genome AF: 0.000322 AC: 49AN: 152288Hom.: 0 Cov.: 34 AF XY: 0.000443 AC XY: 33AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at