rs10237272

Positions:

• chr7-93572590-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001742.4(CALCR):​c.-27+1699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,954 control chromosomes in the GnomAD database, including 31,262 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 0.62 (31262 hom., cov: 32)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALCR	NM_001742.4	c.-27+1699G>A		intron_variant		ENST00000426151.7	NP_001733.1
CALCR	NM_001164737.3	c.-98+1699G>A		intron_variant			NP_001158209.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCR	ENST00000426151.7	c.-27+1699G>A		intron_variant		1	NM_001742.4	ENSP00000389295	P1
CALCR	ENST00000649521.1	c.-98+1699G>A		intron_variant				ENSP00000497687

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94576 AN: 151836 Hom.: 31213 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.623 AC: 94683 AN: 151954 Hom.: 31262 Cov.: 32 AF XY: 0.617 AC XY: 45781 AN XY: 74232

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.591

Alfa AF: 0.542 Hom.: 36410

Bravo AF: 0.640

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10237272; hg19: chr7-93201902;