Genetic Variant CD207:p.Pro328Pro (chr2-70831053-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

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

The NM_015717.5(CD207):c.984G>A(p.Pro328Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,611,962 control chromosomes in the GnomAD database, including 55,972 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.24 ( 4527 hom., cov: 32)

Exomes 𝑓: 0.26 ( 51445 hom. )

Consequence

CD207
NM_015717.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.06

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=-0.81).

BP6

Variant 2-70831053-C-T is Benign according to our data. Variant chr2-70831053-C-T is described in ClinVar as [Benign]. Clinvar id is 3060971.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-2.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD207	NM_015717.5 link	c.984G>A	p.Pro328Pro	synonymous_variant	Exon 6 of 6	ENST00000410009.5	NP_056532.4	Q9UJ71
CD207	XM_011532875.3 link	c.851-132G>A		intron_variant	Intron 6 of 6		XP_011531177.1
CD207	XM_011532876.3 link	c.836+648G>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.984G>A	p.Pro328Pro	synonymous_variant	Exon 6 of 6	1	NM_015717.5	ENSP00000386378.3		Q9UJ71

Frequencies

GnomAD3 genomes

AF:

0.236

AC:

35802

AN:

151938

Hom.:

4522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.244

GnomAD3 exomes

AF:

0.213

AC:

52918

AN:

248124

Hom.:

6632

AF XY:

0.217

AC XY:

29214

AN XY:

134528

show subpopulations

Gnomad AFR exome

AF:

0.215

Gnomad AMR exome

AF:

0.124

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.00100

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.218

Gnomad NFE exome

AF:

0.281

Gnomad OTH exome

AF:

0.232

GnomAD4 exome

AF:

0.257

AC:

375762

AN:

1459906

Hom.:

51445

Cov.:

AF XY:

0.255

AC XY:

185210

AN XY:

726162

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.132

Gnomad4 ASJ exome

AF:

0.272

Gnomad4 EAS exome

AF:

0.000882

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.241

GnomAD4 genome

AF:

0.236

AC:

35822

AN:

152056

Hom.:

4527

Cov.:

AF XY:

0.230

AC XY:

17093

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.191

Gnomad4 ASJ

AF:

0.264

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.151

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.269

Hom.:

11009

Bravo

AF:

0.230

Asia WGS

AF:

0.103

AC:

360

AN:

3478

EpiCase

AF:

0.283

EpiControl

AF:

0.285

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CD207-related disorder

Benign:1

Oct 21, 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

-0.81

CADD

Benign

0.24

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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