chr7-93434389-G-GAAAA

Position:

• chr7-93434389-G-GAAAA

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_1150-95insTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0311 in 507,760 control chromosomes in the GnomAD database, including 301 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.054 (278 hom., cov: 0)
  • Exomes 𝑓: 0.023 (23 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-GAAAA is Benign according to our data. Variant chr7-93434389-G-GAAAA is described in ClinVar as [Benign]. Clinvar id is 1270922.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 7322 AN: 135332 Hom.: 278 Cov.: 0

Gnomad AFR AF: 0.0530

Gnomad AMI AF: 0.0494

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0490

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0509

GnomAD4 exome AF: 0.0227 AC: 8463 AN: 372386 Hom.: 23 AF XY: 0.0214 AC XY: 4226 AN XY: 197186

Gnomad4 AFR exome AF: 0.0271

Gnomad4 AMR exome AF: 0.0790

Gnomad4 ASJ exome AF: 0.00875

Gnomad4 EAS exome AF: 0.0332

Gnomad4 SAS exome AF: 0.00887

Gnomad4 FIN exome AF: 0.0392

Gnomad4 NFE exome AF: 0.0180

Gnomad4 OTH exome AF: 0.0243

GnomAD4 genome AF: 0.0541 AC: 7327 AN: 135374 Hom.: 278 Cov.: 0 AF XY: 0.0561 AC XY: 3654 AN XY: 65124

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.0293

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0504

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 19, 2021

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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;