7-93434389-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001742.4(CALCR):c.1150-96_1150-95insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 492,844 control chromosomes in the GnomAD database, including 3,746 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3412 hom., cov: 0)
  • Exomes 𝑓: 0.21 (334 hom.)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.590

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 -10 ACMG points.

• BP6: Variant 7-93434389-G-GA is Benign according to our data. Variant chr7-93434389-G-GA is described in ClinVar as [Benign]. Clinvar id is 1243938.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALCR	NM_001742.4	c.1150-96_1150-95insT		intron_variant		ENST00000426151.7
CALCR	NM_001164737.3	c.1198-96_1198-95insT		intron_variant
CALCR	NM_001164738.2	c.1150-96_1150-95insT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCR	ENST00000426151.7	c.1150-96_1150-95insT		intron_variant		1	NM_001742.4	P1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 27110 AN: 135470 Hom.: 3411 Cov.: 0

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.207 AC: 73851 AN: 357336 Hom.: 334 AF XY: 0.207 AC XY: 39108 AN XY: 189156

Gnomad4 AFR exome AF: 0.299

Gnomad4 AMR exome AF: 0.215

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.391

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.140

Gnomad4 NFE exome AF: 0.180

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.200 AC: 27120 AN: 135508 Hom.: 3412 Cov.: 0 AF XY: 0.203 AC XY: 13269 AN XY: 65216

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.209

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs200558502; hg19: chr7-93063701;