2-46612348-G-GA
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_002643.4(PIGF):c.321-5dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 782,374 control chromosomes in the GnomAD database, including 3 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002643.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGF | NM_002643.4 | c.321-5dupT | splice_region_variant, intron_variant | Intron 3 of 5 | ENST00000281382.11 | NP_002634.1 | ||
PIGF | NM_173074.3 | c.321-5dupT | splice_region_variant, intron_variant | Intron 3 of 6 | NP_775097.1 | |||
PIGF | XM_011532908.4 | c.321-5dupT | splice_region_variant, intron_variant | Intron 3 of 6 | XP_011531210.1 | |||
PIGF | XM_005264369.4 | c.321-5dupT | splice_region_variant, intron_variant | Intron 3 of 5 | XP_005264426.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGF | ENST00000281382.11 | c.321-5_321-4insT | splice_region_variant, intron_variant | Intron 3 of 5 | 1 | NM_002643.4 | ENSP00000281382.6 | |||
PIGF | ENST00000306465.8 | c.321-5_321-4insT | splice_region_variant, intron_variant | Intron 3 of 6 | 1 | ENSP00000302663.4 | ||||
PIGF | ENST00000412717.1 | n.229-5_229-4insT | splice_region_variant, intron_variant | Intron 2 of 4 | 3 | ENSP00000413202.1 | ||||
PIGF | ENST00000495933.1 | n.3338-5_3338-4insT | splice_region_variant, intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000225 AC: 30AN: 133302Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0590 AC: 3282AN: 55674Hom.: 0 AF XY: 0.0667 AC XY: 1967AN XY: 29510
GnomAD4 exome AF: 0.0559 AC: 36277AN: 649020Hom.: 3 Cov.: 10 AF XY: 0.0573 AC XY: 18956AN XY: 330668
GnomAD4 genome AF: 0.000232 AC: 31AN: 133354Hom.: 0 Cov.: 32 AF XY: 0.000233 AC XY: 15AN XY: 64360
ClinVar
Submissions by phenotype
PIGF-related condition Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at