rs2023772

chr7-93501850-A-Cchr7-93501850-A-G

Variant summary

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

The NM_001742.4(CALCR):c.-26-14843T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,918 control chromosomes in the GnomAD database, including 28,377 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 0.59 (28377 hom., cov: 32)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALCR	NM_001742.4	c.-26-14843T>G		intron_variant		ENST00000426151.7
CALCR	NM_001164737.3	c.-97-5876T>G		intron_variant
CALCR	NM_001164738.2	c.-26-14843T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCR	ENST00000426151.7	c.-26-14843T>G		intron_variant		1	NM_001742.4	P1
CALCR	ENST00000394441.5	c.-26-14843T>G		intron_variant		1		P1
CALCR	ENST00000649521.1	c.-97-5876T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89980 AN: 151800 Hom.: 28327 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.593 AC: 90084 AN: 151918 Hom.: 28377 Cov.: 32 AF XY: 0.589 AC XY: 43710 AN XY: 74204

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.580

Alfa AF: 0.518 Hom.: 26967

Bravo AF: 0.599

Asia WGS AF: 0.655 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.5
Dann	Benign	0.46

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: rs2023772; hg19: chr7-93131162;