5-75360350-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000859.3(HMGCR):c.*8G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 1,610,820 control chromosomes in the GnomAD database, including 7,975 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000859.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMGCR | NM_000859.3 | c.*8G>A | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000287936.9 | NP_000850.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0818 AC: 12431AN: 152052Hom.: 591 Cov.: 32
GnomAD3 exomes AF: 0.104 AC: 25777AN: 248668Hom.: 1576 AF XY: 0.105 AC XY: 14053AN XY: 134360
GnomAD4 exome AF: 0.0963 AC: 140447AN: 1458650Hom.: 7383 Cov.: 31 AF XY: 0.0975 AC XY: 70774AN XY: 725698
GnomAD4 genome AF: 0.0817 AC: 12427AN: 152170Hom.: 592 Cov.: 32 AF XY: 0.0829 AC XY: 6167AN XY: 74402
ClinVar
Submissions by phenotype
HMGCR-related disorder Benign:1
This variant is classified as 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