rs72646506
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_174936.4(PCSK9):c.657+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,613,650 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 Benign (★★).
Frequency
Consequence
NM_174936.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCSK9 | NM_174936.4 | c.657+7A>C | splice_region_variant, intron_variant | ENST00000302118.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCSK9 | ENST00000302118.5 | c.657+7A>C | splice_region_variant, intron_variant | 1 | NM_174936.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000957 AC: 24AN: 250776Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135660
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461452Hom.: 1 Cov.: 35 AF XY: 0.0000426 AC XY: 31AN XY: 727032
GnomAD4 genome AF: 0.000466 AC: 71AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000511 AC XY: 38AN XY: 74410
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 07, 2023 | - - |
Hypercholesterolemia, autosomal dominant, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at