Genetic Variant CALCR:c.1150-302_1150-301dupTT (chr7-93434594-G-GAA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001742.4(CALCR):c.1150-302_1150-301dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 146,826 control chromosomes in the GnomAD database, including 3,043 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3043 hom., cov: 22)

Consequence

CALCR
NM_001742.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.868

Publications

0 publications found

Variant links:

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)

CALCR links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 7-93434594-G-GAA is Benign according to our data. Variant chr7-93434594-G-GAA is described in ClinVar as Benign. ClinVar VariationId is 1222864.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CALCR	NM_001742.4	MANE Select	c.1150-302_1150-301dupTT	intron	N/A	NP_001733.1	P30988-2
CALCR	NM_001164737.3		c.1198-302_1198-301dupTT	intron	N/A	NP_001158209.2	A0A0A0MSQ7
CALCR	NM_001164738.2		c.1150-302_1150-301dupTT	intron	N/A	NP_001158210.1	P30988-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CALCR	ENST00000426151.7	TSL:1 MANE Select	c.1150-301_1150-300insTT	intron	N/A	ENSP00000389295.1	P30988-2
CALCR	ENST00000394441.5	TSL:1	c.1150-301_1150-300insTT	intron	N/A	ENSP00000377959.1	P30988-2
CALCR	ENST00000415529.2	TSL:1	n.375-301_375-300insTT	intron	N/A	ENSP00000413179.1	P30988-5

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

28809

AN:

146766

Hom.:

3042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.208

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

GnomAD4 genome

AF:

0.196

AC:

28822

AN:

146826

Hom.:

3043

Cov.:

AF XY:

0.202

AC XY:

14397

AN XY:

71388

show subpopulations

African (AFR)

AF:

0.136

AC:

5473

AN:

40120

American (AMR)

AF:

0.280

AC:

4159

AN:

14830

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

536

AN:

3412

East Asian (EAS)

AF:

0.389

AC:

1963

AN:

5046

South Asian (SAS)

AF:

0.254

AC:

1180

AN:

4642

European-Finnish (FIN)

AF:

0.223

AC:

2063

AN:

9256

Middle Eastern (MID)

AF:

0.184

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.194

AC:

12880

AN:

66350

Other (OTH)

AF:

0.210

AC:

422

AN:

2006

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

1061

2122

3182

4243

5304

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0727

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.87

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over