rs9690762

Variant names:

• chr7-93486438-A-G
• rs9690762
• NM_001742.4:c.51+493T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-93486438-A-G
• chr7-93486438-A-T

Variant summary

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

The NM_001742.4(CALCR):​c.51+493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,310 control chromosomes in the GnomAD database, including 21,479 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 0.53 (21479 hom., cov: 32)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001742.4. 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
	CALCR	NM_001742.4	MANE Select	c.51+493T>C		intron	N/A	NP_001733.1	P30988-2
	CALCR	NM_001164737.3		c.51+493T>C		intron	N/A	NP_001158209.2	A0A0A0MSQ7
	CALCR	NM_001164738.2		c.51+493T>C		intron	N/A	NP_001158210.1	P30988-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALCR	ENST00000426151.7	TSL:1 MANE Select	c.51+493T>C		intron	N/A	ENSP00000389295.1	P30988-2
	CALCR	ENST00000394441.5	TSL:1	c.51+493T>C		intron	N/A	ENSP00000377959.1	P30988-2
	CALCR	ENST00000415529.2	TSL:1	n.51+493T>C		intron	N/A	ENSP00000413179.1	P30988-5

Frequencies

GnomAD3 genomes AF: 0.529 AC: 79975 AN: 151192 Hom.: 21457 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.529 AC: 80039 AN: 151310 Hom.: 21479 Cov.: 32 AF XY: 0.525 AC XY: 38820 AN XY: 73920

African (AFR) AF: 0.608 AC: 25166 AN: 41378

American (AMR) AF: 0.436 AC: 6598 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1821 AN: 3454

East Asian (EAS) AF: 0.691 AC: 3516 AN: 5090

South Asian (SAS) AF: 0.580 AC: 2792 AN: 4810

European-Finnish (FIN) AF: 0.452 AC: 4779 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33585 AN: 67572

Other (OTH) AF: 0.534 AC: 1120 AN: 2098

Alfa AF: 0.516 Hom.: 2627

Bravo AF: 0.528

Asia WGS AF: 0.605 AC: 2097 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.80
PhyloP100		-1.4
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: rs9690762; hg19: chr7-93115750;