rs10045497

Variant names:

• chr5-75340659-C-A
• rs10045497
• NM_000859.3:c.-23-1924C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-75340659-C-A
• chr5-75340659-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000859.3(HMGCR):​c.-23-1924C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,982 control chromosomes in the GnomAD database, including 10,109 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (10109 hom., cov: 32)
• Consequence: HMGCR NM_000859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 22 publications found

Genes affected

HMGCR (HGNC:5006): (3-hydroxy-3-methylglutaryl-CoA reductase) HMG-CoA reductase is the rate-limiting enzyme for cholesterol synthesis and is regulated via a negative feedback mechanism mediated by sterols and non-sterol metabolites derived from mevalonate, the product of the reaction catalyzed by reductase. Normally in mammalian cells this enzyme is suppressed by cholesterol derived from the internalization and degradation of low density lipoprotein (LDL) via the LDL receptor. Competitive inhibitors of the reductase induce the expression of LDL receptors in the liver, which in turn increases the catabolism of plasma LDL and lowers the plasma concentration of cholesterol, an important determinant of atherosclerosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

HMGCR Gene-Disease associations (from GenCC):

• muscular dystrophy, limb-girdle, autosomal recessive 28

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000859.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGCR	NM_000859.3	MANE Select	c.-23-1924C>A		intron	N/A	NP_000850.1
	HMGCR	NM_001364187.1		c.-23-1924C>A		intron	N/A	NP_001351116.1
	HMGCR	NM_001130996.2		c.-23-1924C>A		intron	N/A	NP_001124468.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMGCR	ENST00000287936.9	TSL:1 MANE Select	c.-23-1924C>A		intron	N/A	ENSP00000287936.4
	HMGCR	ENST00000343975.9	TSL:1	c.-23-1924C>A		intron	N/A	ENSP00000340816.5
	HMGCR	ENST00000680940.1		c.-53C>A		5_prime_UTR	Exon 2 of 21	ENSP00000505561.1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53750 AN: 151864 Hom.: 10103 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.348

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53785 AN: 151982 Hom.: 10109 Cov.: 32 AF XY: 0.362 AC XY: 26862 AN XY: 74272

African (AFR) AF: 0.235 AC: 9731 AN: 41480

American (AMR) AF: 0.376 AC: 5741 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2623 AN: 5166

South Asian (SAS) AF: 0.545 AC: 2626 AN: 4822

European-Finnish (FIN) AF: 0.441 AC: 4642 AN: 10530

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25712 AN: 67930

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.367 Hom.: 1339

Bravo AF: 0.339

Asia WGS AF: 0.508 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10045497; hg19: chr5-74636484; COSMIC: COSV55314837; COSMIC: COSV55314837;