Variant rs11118555 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_172351.3(CD46):c.857-271T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,048,048 control chromosomes in the GnomAD database, including 6,837 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.094 ( 910 hom., cov: 32)

Exomes 𝑓: 0.11 ( 5927 hom. )

Consequence

CD46
NM_172351.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.162

Variant links:

Genes affected

CD46 (HGNC:6953): (CD46 molecule) The protein encoded by this gene is a type I membrane protein and is a regulatory part of the complement system. The encoded protein has cofactor activity for inactivation of complement components C3b and C4b by serum factor I, which protects the host cell from damage by complement. In addition, the encoded protein can act as a receptor for the Edmonston strain of measles virus, human herpesvirus-6, and type IV pili of pathogenic Neisseria. Finally, the protein encoded by this gene may be involved in the fusion of the spermatozoa with the oocyte during fertilization. Mutations at this locus have been associated with susceptibility to hemolytic uremic syndrome. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2010]

CD46 links:

MIR29B2CHG (HGNC:32018): (MIR29B2 and MIR29C host gene)

MIR29B2CHG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

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

BP6

Variant 1-207767508-T-A is Benign according to our data. Variant chr1-207767508-T-A is described in ClinVar as [Benign]. Clinvar id is 1289553.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD46	NM_172351.3 linkuse as main transcript	c.857-271T>A		intron_variant		ENST00000367042.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD46	ENST00000367042.6 linkuse as main transcript	c.857-271T>A		intron_variant		1	NM_172351.3	A2	P15529-11
MIR29B2CHG	ENST00000710901.1 linkuse as main transcript	n.663-4520A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0938

AC:

14256

AN:

152034

Hom.:

910

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0216

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.168

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0794

Gnomad SAS

AF:

0.0911

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.0942

GnomAD4 exome

AF:

0.110

AC:

98766

AN:

895896

Hom.:

5927

Cov.:

AF XY:

0.109

AC XY:

50793

AN XY:

468098

show subpopulations

Gnomad4 AFR exome

AF:

0.0212

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.0846

Gnomad4 SAS exome

AF:

0.0893

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.0994

GnomAD4 genome

AF:

0.0937

AC:

14261

AN:

152152

Hom.:

910

Cov.:

AF XY:

0.0982

AC XY:

7300

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0215

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0793

Gnomad4 SAS

AF:

0.0916

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.110

Gnomad4 OTH

AF:

0.0927

Alfa

AF:

0.103

Hom.:

131

Bravo

AF:

0.0917

Asia WGS

AF:

0.0840

AC:

294

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.0

DANN

Benign

0.80

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

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