7-93575232-C-T

Variant names:

• chr7-93575232-C-T
• rs2528521
• ENST00000887175.1:c.-970G>A

Variant summary

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

The ENST00000887175.1(CALCR):​c.-970G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,860 control chromosomes in the GnomAD database, including 24,324 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 0.55 (24324 hom., cov: 31)
• Consequence: CALCR ENST00000887175.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 9 publications found

Genes affected

CALCR (HGNC:1440): (calcitonin receptor) This gene encodes a high affinity receptor for the peptide hormone calcitonin and belongs to a subfamily of seven transmembrane-spanning G protein-coupled receptors. The encoded protein is involved in maintaining calcium homeostasis and in regulating osteoclast-mediated bone resorption. Polymorphisms in this gene have been associated with variations in bone mineral density and onset of osteoporosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

CALCR Gene-Disease associations (from GenCC):

• osteoporosis

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000887175.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCR	ENST00000887175.1		c.-970G>A		5_prime_UTR	Exon 1 of 13	ENSP00000557234.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82747 AN: 151742 Hom.: 24296 Cov.: 31

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.545 AC: 82835 AN: 151860 Hom.: 24324 Cov.: 31 AF XY: 0.541 AC XY: 40152 AN XY: 74196

African (AFR) AF: 0.773 AC: 31974 AN: 41380

American (AMR) AF: 0.488 AC: 7444 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3403 AN: 5120

South Asian (SAS) AF: 0.572 AC: 2745 AN: 4798

European-Finnish (FIN) AF: 0.374 AC: 3951 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30172 AN: 67962

Other (OTH) AF: 0.509 AC: 1073 AN: 2108

Alfa AF: 0.608 Hom.: 6909

Bravo AF: 0.561

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.7
DANN	Benign	0.76
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2528521; hg19: chr7-93204544;