Genetic Variant NM_015717.5:c.711T>C (chr2-70832906-A-G) – 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.711T>C(p.Ser237Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 1,612,684 control chromosomes in the GnomAD database, including 9,552 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.14 ( 2204 hom., cov: 32)

Exomes 𝑓: 0.091 ( 7348 hom. )

Consequence

CD207
NM_015717.5 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.49

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=-0.82).

BP6

Variant 2-70832906-A-G is Benign according to our data. Variant chr2-70832906-A-G is described in ClinVar as [Benign]. Clinvar id is 3059699.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.49 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD207	NM_015717.5 link	c.711T>C	p.Ser237Ser	synonymous_variant	Exon 4 of 6	ENST00000410009.5	NP_056532.4	Q9UJ71
CD207	XM_011532875.3 link	c.711T>C	p.Ser237Ser	synonymous_variant	Exon 4 of 7		XP_011531177.1
CD207	XM_011532876.3 link	c.711T>C	p.Ser237Ser	synonymous_variant	Exon 4 of 6		XP_011531178.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD207	ENST00000410009.5 link	c.711T>C	p.Ser237Ser	synonymous_variant	Exon 4 of 6	1	NM_015717.5	ENSP00000386378.3		Q9UJ71

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21237

AN:

151846

Hom.:

2197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.0769

Gnomad AMR

AF:

0.0959

Gnomad ASJ

AF:

0.0753

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.0565

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0780

Gnomad OTH

AF:

0.137

GnomAD3 exomes

AF:

0.0991

AC:

24629

AN:

248462

Hom.:

1701

AF XY:

0.100

AC XY:

13527

AN XY:

134788

show subpopulations

Gnomad AFR exome

AF:

0.284

Gnomad AMR exome

AF:

0.0580

Gnomad ASJ exome

AF:

0.0791

Gnomad EAS exome

AF:

0.118

Gnomad SAS exome

AF:

0.161

Gnomad FIN exome

AF:

0.0537

Gnomad NFE exome

AF:

0.0771

Gnomad OTH exome

AF:

0.0972

GnomAD4 exome

AF:

0.0909

AC:

132844

AN:

1460720

Hom.:

7348

Cov.:

AF XY:

0.0928

AC XY:

67397

AN XY:

726620

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.0607

Gnomad4 ASJ exome

AF:

0.0805

Gnomad4 EAS exome

AF:

0.120

Gnomad4 SAS exome

AF:

0.161

Gnomad4 FIN exome

AF:

0.0530

Gnomad4 NFE exome

AF:

0.0809

Gnomad4 OTH exome

AF:

0.105

GnomAD4 genome

AF:

0.140

AC:

21266

AN:

151964

Hom.:

2204

Cov.:

AF XY:

0.138

AC XY:

10270

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.0957

Gnomad4 ASJ

AF:

0.0753

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.0565

Gnomad4 NFE

AF:

0.0779

Gnomad4 OTH

AF:

0.136

Alfa

AF:

0.0925

Hom.:

943

Bravo

AF:

0.146

Asia WGS

AF:

0.127

AC:

440

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CD207-related disorder

Benign:1

Nov 06, 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

-0.82

CADD

Benign

3.8

DANN

Benign

0.53

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