Variant chr12-7090354-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001733.7(C1R):c.232-106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 628,710 control chromosomes in the GnomAD database, including 42,355 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11293 hom., cov: 32)

Exomes 𝑓: 0.36 ( 31062 hom. )

Consequence

C1R
NM_001733.7 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.156

Variant links:

Genes affected

C1R (HGNC:1246): (complement C1r) This gene encodes a member of the peptidase S1 protein family. The encoded protein is a proteolytic subunit in the complement system C1 complex. The complement system acts as a mediator in the innate immune response by ultimately triggering phagocytosis, inflammation, and rupturing the bacterial cell wall. Mutations in this gene are associated with Ehlers-Danlos Syndrome. [provided by RefSeq, Dec 2018]

C1R links:

C1RL (HGNC:21265): (complement C1r subcomponent like) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in zymogen activation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

C1RL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 12-7090354-A-G is Benign according to our data. Variant chr12-7090354-A-G is described in ClinVar as [Benign]. Clinvar id is 1273291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1R	NM_001733.7 linkuse as main transcript	c.232-106T>C		intron_variant		ENST00000647956.2	NP_001724.4
C1R	NM_001354346.2 linkuse as main transcript	c.274-106T>C		intron_variant			NP_001341275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1R	ENST00000647956.2 linkuse as main transcript	c.232-106T>C		intron_variant			NM_001733.7	ENSP00000497341	P1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57657

AN:

151984

Hom.:

11295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.352

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.341

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.356

AC:

169760

AN:

476608

Hom.:

31062

Cov.:

AF XY:

0.355

AC XY:

89624

AN XY:

252202

show subpopulations

Gnomad4 AFR exome

AF:

0.448

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.351

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.345

Gnomad4 FIN exome

AF:

0.371

Gnomad4 NFE exome

AF:

0.352

Gnomad4 OTH exome

AF:

0.362

GnomAD4 genome

AF:

0.379

AC:

57680

AN:

152102

Hom.:

11293

Cov.:

AF XY:

0.379

AC XY:

28199

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.453

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.352

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.341

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.373

Hom.:

2198

Bravo

AF:

0.373

Asia WGS

AF:

0.396

AC:

1379

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.3

DANN

Benign

0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over