rs138727736

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_012120.3(CD2AP):c.1120A>G(p.Thr374Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00549 in 1,612,002 control chromosomes in the GnomAD database, including 48 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 Likely benign (★★).

Frequency

Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 47 hom. )

Consequence

CD2AP
NM_012120.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

CD2AP (HGNC:14258): (CD2 associated protein) This gene encodes a scaffolding molecule that regulates the actin cytoskeleton. The protein directly interacts with filamentous actin and a variety of cell membrane proteins through multiple actin binding sites, SH3 domains, and a proline-rich region containing binding sites for SH3 domains. The cytoplasmic protein localizes to membrane ruffles, lipid rafts, and the leading edges of cells. It is implicated in dynamic actin remodeling and membrane trafficking that occurs during receptor endocytosis and cytokinesis. Haploinsufficiency of this gene is implicated in susceptibility to glomerular disease. [provided by RefSeq, Jul 2008]

CD2AP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0028515756).

BP6

Variant 6-47595872-A-G is Benign according to our data. Variant chr6-47595872-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 260180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-47595872-A-G is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00365 (556/152186) while in subpopulation SAS AF= 0.0127 (61/4818). AF 95% confidence interval is 0.0101. There are 1 homozygotes in gnomad4. There are 251 alleles in male gnomad4 subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CD2AP	NM_012120.3 linkuse as main transcript	c.1120A>G	p.Thr374Ala	missense_variant	12/18	ENST00000359314.5
CD2AP	XM_005248976.2 linkuse as main transcript	c.1108A>G	p.Thr370Ala	missense_variant	12/18
CD2AP	XM_011514449.3 linkuse as main transcript	c.973A>G	p.Thr325Ala	missense_variant	11/17
CD2AP	XM_017010641.2 linkuse as main transcript	c.1120A>G	p.Thr374Ala	missense_variant	12/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD2AP	ENST00000359314.5 linkuse as main transcript	c.1120A>G	p.Thr374Ala	missense_variant	12/18	1	NM_012120.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00368

AC:

559

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00393

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0127

Gnomad FIN

AF:

0.000659

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00538

Gnomad OTH

AF:

0.00384

GnomAD3 exomes

AF:

0.00508

AC:

1274

AN:

250646

Hom.:

AF XY:

0.00587

AC XY:

795

AN XY:

135500

show subpopulations

Gnomad AFR exome

AF:

0.000927

Gnomad AMR exome

AF:

0.00369

Gnomad ASJ exome

AF:

0.00428

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0145

Gnomad FIN exome

AF:

0.000509

Gnomad NFE exome

AF:

0.00515

Gnomad OTH exome

AF:

0.00818

GnomAD4 exome

AF:

0.00568

AC:

8290

AN:

1459816

Hom.:

Cov.:

AF XY:

0.00606

AC XY:

4405

AN XY:

726322

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00338

Gnomad4 ASJ exome

AF:

0.00376

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0162

Gnomad4 FIN exome

AF:

0.000768

Gnomad4 NFE exome

AF:

0.00544

Gnomad4 OTH exome

AF:

0.00640

GnomAD4 genome

AF:

0.00365

AC:

556

AN:

152186

Hom.:

Cov.:

AF XY:

0.00337

AC XY:

251

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.000987

Gnomad4 AMR

AF:

0.00393

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0127

Gnomad4 FIN

AF:

0.000659

Gnomad4 NFE

AF:

0.00537

Gnomad4 OTH

AF:

0.00380

Alfa

AF:

0.00526

Hom.:

Bravo

AF:

0.00349

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00535

AC:

ExAC

AF:

0.00502

AC:

609

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.00694

EpiControl

AF:

0.00616

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2022	CD2AP: BP4, BS1, BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Dec 26, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 13, 2020	This variant is associated with the following publications: (PMID: 19131354, 27884173, 26997877) -

Focal segmental glomerulosclerosis 3, susceptibility to

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Focal segmental glomerulosclerosis

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Sep 28, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.059

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.81

Cadd

Benign

0.081

Dann

Benign

0.40

DEOGEN2

Benign

0.12

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.41

MetaRNN

Benign

0.0029

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.49

MutationTaster

Benign

1.0

PrimateAI

Benign

0.25

PROVEAN

Benign

0.47

REVEL

Benign

0.064

Sift

Benign

0.73

Sift4G

Benign

0.77

Polyphen

0.0

Vest4

0.022

MVP

0.25

MPC

0.070

ClinPred

0.00027

GERP RS

-5.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.016

gMVP

0.099

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