Variant chr2-70831095-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_015717.5(CD207):c.942G>A(p.Thr314Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,612,600 control chromosomes in the GnomAD database, including 48,170 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.19 ( 3273 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44897 hom. )

Consequence

CD207
NM_015717.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.34

Variant links:

Genes affected

CD207 (HGNC:17935): (CD207 molecule) The protein encoded by this gene is expressed only in Langerhans cells which are immature dendritic cells of the epidermis and mucosa. It is localized in the Birbeck granules, organelles present in the cytoplasm of Langerhans cells and consisting of superimposed and zippered membranes. It is a C-type lectin with mannose binding specificity, and it has been proposed that mannose binding by this protein leads to internalization of antigen into Birbeck granules and providing access to a nonclassical antigen-processing pathway. Mutations in this gene result in Birbeck granules deficiency or loss of sugar binding activity. [provided by RefSeq, Aug 2010]

CD207 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 2-70831095-C-T is Benign according to our data. Variant chr2-70831095-C-T is described in ClinVar as [Benign]. Clinvar id is 3060627.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.34 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD207	NM_015717.5 link	c.942G>A	p.Thr314Thr	synonymous_variant	Exon 6 of 6	ENST00000410009.5	NP_056532.4	Q9UJ71
CD207	XM_011532875.3 link	c.850+92G>A		intron_variant	Intron 6 of 6		XP_011531177.1
CD207	XM_011532876.3 link	c.836+606G>A		intron_variant	Intron 5 of 5		XP_011531178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD207	ENST00000410009.5 link	c.942G>A	p.Thr314Thr	synonymous_variant	Exon 6 of 6	1	NM_015717.5	ENSP00000386378.3		Q9UJ71

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

28940

AN:

151862

Hom.:

3267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0724

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.0805

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.189

GnomAD3 exomes

AF:

0.222

AC:

55173

AN:

248998

Hom.:

6765

AF XY:

0.221

AC XY:

29829

AN XY:

135094

show subpopulations

Gnomad AFR exome

AF:

0.0673

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.0816

Gnomad SAS exome

AF:

0.185

Gnomad FIN exome

AF:

0.219

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.233

GnomAD4 exome

AF:

0.243

AC:

354639

AN:

1460620

Hom.:

44897

Cov.:

AF XY:

0.241

AC XY:

175352

AN XY:

726628

show subpopulations

Gnomad4 AFR exome

AF:

0.0691

Gnomad4 AMR exome

AF:

0.273

Gnomad4 ASJ exome

AF:

0.253

Gnomad4 EAS exome

AF:

0.0763

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.191

AC:

28962

AN:

151980

Hom.:

3273

Cov.:

AF XY:

0.187

AC XY:

13870

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.0723

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.0803

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

0.221

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.232

Hom.:

6089

Bravo

AF:

0.187

Asia WGS

AF:

0.163

AC:

567

AN:

3478

EpiCase

AF:

0.245

EpiControl

AF:

0.242

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CD207-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.35

DANN

Benign

0.44

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