NM_000859.3:c.2660C>T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_000859.3(HMGCR):c.2660C>T(p.Thr887Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000859.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HMGCR | NM_000859.3 | c.2660C>T | p.Thr887Ile | missense_variant | Exon 20 of 20 | ENST00000287936.9 | NP_000850.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250066Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135112
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461422Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726978
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2660C>T (p.T887I) alteration is located in exon 20 (coding exon 19) of the HMGCR gene. This alteration results from a C to T substitution at nucleotide position 2660, causing the threonine (T) at amino acid position 887 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at