7-93435824-TAATA-T

Variant summary

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

The NM_001742.4(CALCR):c.1149+124_1149+127del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 310,956 control chromosomes in the GnomAD database, including 458 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.031 (219 hom., cov: 22)
  • Exomes 𝑓: 0.025 (239 hom.)
• Consequence: CALCR NM_001742.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0170

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 7-93435824-TAATA-T is Benign according to our data. Variant chr7-93435824-TAATA-T is described in ClinVar as [Benign]. Clinvar id is 1263502.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALCR	NM_001742.4	c.1149+124_1149+127del		intron_variant		ENST00000426151.7
CALCR	NM_001164737.3	c.1197+124_1197+127del		intron_variant
CALCR	NM_001164738.2	c.1149+124_1149+127del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALCR	ENST00000426151.7	c.1149+124_1149+127del		intron_variant		1	NM_001742.4	P1

Frequencies

GnomAD3 genomes AF: 0.0313 AC: 4539 AN: 145076 Hom.: 220 Cov.: 22

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.00695

Gnomad EAS AF: 0.00122

Gnomad SAS AF: 0.00425

Gnomad FIN AF: 0.00601

Gnomad MID AF: 0.0296

Gnomad NFE AF: 0.00350

Gnomad OTH AF: 0.0268

GnomAD4 exome AF: 0.0253 AC: 4196 AN: 165800 Hom.: 239 AF XY: 0.0237 AC XY: 2106 AN XY: 88840

Gnomad4 AFR exome AF: 0.0849

Gnomad4 AMR exome AF: 0.0289

Gnomad4 ASJ exome AF: 0.0206

Gnomad4 EAS exome AF: 0.00484

Gnomad4 SAS exome AF: 0.0408

Gnomad4 FIN exome AF: 0.0710

Gnomad4 NFE exome AF: 0.0176

Gnomad4 OTH exome AF: 0.0246

GnomAD4 genome AF: 0.0313 AC: 4545 AN: 145156 Hom.: 219 Cov.: 22 AF XY: 0.0312 AC XY: 2210 AN XY: 70796

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.00695

Gnomad4 EAS AF: 0.00122

Gnomad4 SAS AF: 0.00426

Gnomad4 FIN AF: 0.00601

Gnomad4 NFE AF: 0.00350

Gnomad4 OTH AF: 0.0265

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: rs140043489; hg19: chr7-93065136;