7-93434389-G-GAA

Position:

• chr7-93434389-G-GAA

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_1150-95insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 502,452 control chromosomes in the GnomAD database, including 2,348 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (1990 hom., cov: 0)
  • Exomes 𝑓: 0.14 (358 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-GAA is Benign according to our data. Variant chr7-93434389-G-GAA is described in ClinVar as [Benign]. Clinvar id is 1274232.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 22049 AN: 135296 Hom.: 1985 Cov.: 0

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.145 AC: 53079 AN: 367116 Hom.: 358 AF XY: 0.145 AC XY: 28131 AN XY: 194376

Gnomad4 AFR exome AF: 0.0690

Gnomad4 AMR exome AF: 0.164

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.293

Gnomad4 SAS exome AF: 0.150

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.140

GnomAD4 genome AF: 0.163 AC: 22052 AN: 135336 Hom.: 1990 Cov.: 0 AF XY: 0.166 AC XY: 10833 AN XY: 65102

Gnomad4 AFR AF: 0.0708

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.169

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

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;