rs9641123

chr7-93568420-G-C

Variant summary

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

The NM_001742.4(CALCR):c.-27+5869C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,640 control chromosomes in the GnomAD database, including 8,180 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 0.30 (8180 hom., cov: 30)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALCR	NM_001742.4	c.-27+5869C>G		intron_variant		ENST00000426151.7
CALCR	NM_001164737.3	c.-98+5869C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCR	ENST00000426151.7	c.-27+5869C>G		intron_variant		1	NM_001742.4	P1
CALCR	ENST00000649521.1	c.-98+5869C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45302 AN: 151522 Hom.: 8183 Cov.: 30

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.299 AC: 45293 AN: 151640 Hom.: 8180 Cov.: 30 AF XY: 0.298 AC XY: 22110 AN XY: 74078

Gnomad4 AFR AF: 0.0867

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.321

Alfa AF: 0.340 Hom.: 1255

Bravo AF: 0.278

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.8
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9641123; hg19: chr7-93197732;