7-93477232-T-C

Position:

• chr7-93477232-T-C

Variant summary

Our verdict is Benign. Variant got -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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALCR	NM_001742.4	c.316+326A>G		intron_variant		ENST00000426151.7	NP_001733.1
CALCR	NM_001164737.3	c.316+326A>G		intron_variant			NP_001158209.2
CALCR	NM_001164738.2	c.316+326A>G		intron_variant			NP_001158210.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CALCR	ENST00000426151.7	c.316+326A>G		intron_variant		1	NM_001742.4	ENSP00000389295.1

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

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0512

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.171

Alfa AF: 0.214 Hom.: 513

Bravo AF: 0.158

Asia WGS AF: 0.0740 AC: 260 AN: 3478

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.76

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: rs17788132; hg19: chr7-93106544;