7-93442113-T-C

Position:

• chr7-93442113-T-C

Variant summary

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

The NM_001742.4(CALCR):​c.802+1491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,934 control chromosomes in the GnomAD database, including 33,572 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 0.66 (33572 hom., cov: 31)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALCR	NM_001742.4	c.802+1491A>G		intron_variant		ENST00000426151.7	NP_001733.1
CALCR	NM_001164737.3	c.850+1491A>G		intron_variant			NP_001158209.2
CALCR	NM_001164738.2	c.802+1491A>G		intron_variant			NP_001158210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCR	ENST00000426151.7	c.802+1491A>G		intron_variant		1	NM_001742.4	ENSP00000389295.1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100136 AN: 151814 Hom.: 33556 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.660 AC: 100209 AN: 151934 Hom.: 33572 Cov.: 31 AF XY: 0.659 AC XY: 48944 AN XY: 74232

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.706

Alfa AF: 0.566 Hom.: 3704

Bravo AF: 0.685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs757033; hg19: chr7-93071425;