Variant rs1071849 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_001803.3(CD52):c.119A>G(p.Asn40Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 1,612,364 control chromosomes in the GnomAD database, including 428,107 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.70 ( 37065 hom., cov: 31)

Exomes 𝑓: 0.73 ( 391042 hom. )

Consequence

CD52
NM_001803.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.160

Variant links:

Genes affected

CD52 (HGNC:1804): (CD52 molecule) Involved in positive regulation of cytosolic calcium ion concentration. Predicted to be located in extracellular region and plasma membrane. Predicted to be intrinsic component of plasma membrane. Predicted to be active in sperm midpiece. [provided by Alliance of Genome Resources, Apr 2022]

CD52 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 (MetaRNN=4.305119E-7).

BP6

Variant 1-26320235-A-G is Benign according to our data. Variant chr1-26320235-A-G is described in ClinVar as [Benign]. Clinvar id is 3059084.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD52	NM_001803.3 linkuse as main transcript	c.119A>G	p.Asn40Ser	missense_variant	2/2	ENST00000374213.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD52	ENST00000374213.3 linkuse as main transcript	c.119A>G	p.Asn40Ser	missense_variant	2/2	1	NM_001803.3	P1
CD52	ENST00000470468.1 linkuse as main transcript	n.292A>G		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes

AF:

0.695

AC:

105287

AN:

151464

Hom.:

37036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.807

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.770

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.524

Gnomad FIN

AF:

0.697

Gnomad MID

AF:

0.663

Gnomad NFE

AF:

0.755

Gnomad OTH

AF:

0.700

GnomAD3 exomes

AF:

0.669

AC:

167316

AN:

250142

Hom.:

57591

AF XY:

0.671

AC XY:

90821

AN XY:

135254

show subpopulations

Gnomad AFR exome

AF:

0.657

Gnomad AMR exome

AF:

0.574

Gnomad ASJ exome

AF:

0.765

Gnomad EAS exome

AF:

0.424

Gnomad SAS exome

AF:

0.540

Gnomad FIN exome

AF:

0.704

Gnomad NFE exome

AF:

0.756

Gnomad OTH exome

AF:

0.705

GnomAD4 exome

AF:

0.727

AC:

1061658

AN:

1460782

Hom.:

391042

Cov.:

AF XY:

0.723

AC XY:

525084

AN XY:

726712

show subpopulations

Gnomad4 AFR exome

AF:

0.659

Gnomad4 AMR exome

AF:

0.582

Gnomad4 ASJ exome

AF:

0.769

Gnomad4 EAS exome

AF:

0.423

Gnomad4 SAS exome

AF:

0.545

Gnomad4 FIN exome

AF:

0.709

Gnomad4 NFE exome

AF:

0.761

Gnomad4 OTH exome

AF:

0.700

GnomAD4 genome

AF:

0.695

AC:

105365

AN:

151582

Hom.:

37065

Cov.:

AF XY:

0.687

AC XY:

50873

AN XY:

74074

show subpopulations

Gnomad4 AFR

AF:

0.660

Gnomad4 AMR

AF:

0.648

Gnomad4 ASJ

AF:

0.770

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.697

Gnomad4 NFE

AF:

0.754

Gnomad4 OTH

AF:

0.693

Alfa

AF:

0.745

Hom.:

54939

Bravo

AF:

0.693

TwinsUK

AF:

0.766

AC:

2842

ALSPAC

AF:

0.758

AC:

2920

ESP6500AA

AF:

0.667

AC:

2938

ESP6500EA

AF:

0.765

AC:

6583

ExAC

AF:

0.671

AC:

81466

Asia WGS

AF:

0.459

AC:

1598

AN:

3476

EpiCase

AF:

0.758

EpiControl

AF:

0.759

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

CD52-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 16, 2019

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

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.9

DANN

Benign

0.85

DEOGEN2

Benign

0.033

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.010

LIST_S2

Benign

0.38

MetaRNN

Benign

4.3e-7

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.4

REVEL

Benign

0.039

Sift

Benign

1.0

Sift4G

Benign

0.93

Polyphen

0.0090

Vest4

0.021

MPC

0.40

ClinPred

0.0047

GERP RS

-1.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.070

gMVP

0.015

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