dbSNP rs200558502: CALCR:c.1150-100_1150-96delTTTTT (chr7-93434389-GAAAAA-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001742.4(CALCR):c.1150-100_1150-96delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

CALCR
NM_001742.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.696

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.1150-100_1150-96delTTTTT	intron	N/A	NP_001733.1	P30988-2
CALCR	NM_001164737.3		c.1198-100_1198-96delTTTTT	intron	N/A	NP_001158209.2	A0A0A0MSQ7
CALCR	NM_001164738.2		c.1150-100_1150-96delTTTTT	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.1150-100_1150-96delTTTTT	intron	N/A	ENSP00000389295.1	P30988-2
CALCR	ENST00000394441.5	TSL:1	c.1150-100_1150-96delTTTTT	intron	N/A	ENSP00000377959.1	P30988-2
CALCR	ENST00000415529.2	TSL:1	n.375-100_375-96delTTTTT	intron	N/A	ENSP00000413179.1	P30988-5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

376436

Hom.:

AF XY:

0.00

AC XY:

AN XY:

199276

African (AFR)

AF:

0.00

AC:

AN:

10886

American (AMR)

AF:

0.00

AC:

AN:

15876

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12500

East Asian (EAS)

AF:

0.00

AC:

AN:

26256

South Asian (SAS)

AF:

0.00

AC:

AN:

29428

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28154

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2082

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

229402

Other (OTH)

AF:

0.00

AC:

AN:

21852

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.70

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over