rs17788132

Variant names:

• chr7-93477232-T-C
• rs17788132
• NM_001742.4:c.316+326A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-93477232-T-C
• chr7-93477232-T-A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001742.4(CALCR):​c.316+326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 151,840 control chromosomes in the GnomAD database, including 3,289 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (3289 hom., cov: 32)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.653
• Publications: 0 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 7-93477232-T-C is Benign according to our data. Variant chr7-93477232-T-C is described in ClinVar as Benign. ClinVar VariationId is 1246140.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 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.316+326A>G		intron	N/A	NP_001733.1	P30988-2
	CALCR	NM_001164737.3		c.316+326A>G		intron	N/A	NP_001158209.2	A0A0A0MSQ7
	CALCR	NM_001164738.2		c.316+326A>G		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.316+326A>G		intron	N/A	ENSP00000389295.1	P30988-2
	CALCR	ENST00000394441.5	TSL:1	c.316+326A>G		intron	N/A	ENSP00000377959.1	P30988-2
	CALCR	ENST00000415529.2	TSL:1	n.316+326A>G		intron	N/A	ENSP00000413179.1	P30988-5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27453 AN: 151722 Hom.: 3290 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.181 AC: 27450 AN: 151840 Hom.: 3289 Cov.: 32 AF XY: 0.184 AC XY: 13677 AN XY: 74186

African (AFR) AF: 0.0432 AC: 1796 AN: 41528

American (AMR) AF: 0.138 AC: 2096 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3458

East Asian (EAS) AF: 0.0512 AC: 261 AN: 5102

South Asian (SAS) AF: 0.134 AC: 646 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3953 AN: 10548

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17330 AN: 67830

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.152 Hom.: 910

Bravo AF: 0.158

Asia WGS AF: 0.0740 AC: 260 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		-0.65
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: rs17788132; hg19: chr7-93106544;