Variant chr5-150618566-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000394243.5(SYNPO):c.199G>A(p.Asp67Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 1,550,392 control chromosomes in the GnomAD database, including 5,354 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 (★).

Frequency

Genomes: 𝑓 0.094 ( 1577 hom., cov: 32)

Exomes 𝑓: 0.036 ( 3777 hom. )

Consequence

SYNPO
ENST00000394243.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.11

Variant links:

Genes affected

SYNPO (HGNC:30672): (synaptopodin) Synaptopodin is an actin-associated protein that may play a role in actin-based cell shape and motility. The name synaptopodin derives from the protein's associations with postsynaptic densities and dendritic spines and with renal podocytes (Mundel et al., 1997 [PubMed 9314539]).[supplied by OMIM, Mar 2008]

SYNPO 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=0.0036984086).

BP6

Variant 5-150618566-G-A is Benign according to our data. Variant chr5-150618566-G-A is described in ClinVar as [Benign]. Clinvar id is 1283897.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
SYNPO	NM_001166208.2 linkuse as main transcript	c.199G>A	p.Asp67Asn	missense_variant	2/3	NP_001159680.1
SYNPO	NM_001166209.2 linkuse as main transcript	c.199G>A	p.Asp67Asn	missense_variant	2/3	NP_001159681.1
SYNPO	XM_006714755.4 linkuse as main transcript	c.199G>A	p.Asp67Asn	missense_variant	2/4	XP_006714818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNPO	ENST00000394243.5 linkuse as main transcript	c.199G>A	p.Asp67Asn	missense_variant	2/3	1		ENSP00000377789	A2	Q8N3V7-1
SYNPO	ENST00000522122.1 linkuse as main transcript	c.199G>A	p.Asp67Asn	missense_variant	2/3	2		ENSP00000428378	A2	Q8N3V7-1

Frequencies

GnomAD3 genomes

AF:

0.0935

AC:

14224

AN:

152072

Hom.:

1569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0350

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.0275

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.0561

GnomAD3 exomes

AF:

0.0671

AC:

10300

AN:

153396

Hom.:

969

AF XY:

0.0698

AC XY:

5684

AN XY:

81414

show subpopulations

Gnomad AFR exome

AF:

0.251

Gnomad AMR exome

AF:

0.0212

Gnomad ASJ exome

AF:

0.00154

Gnomad EAS exome

AF:

0.265

Gnomad SAS exome

AF:

0.152

Gnomad FIN exome

AF:

0.0307

Gnomad NFE exome

AF:

0.0133

Gnomad OTH exome

AF:

0.0424

GnomAD4 exome

AF:

0.0363

AC:

50747

AN:

1398202

Hom.:

3777

Cov.:

AF XY:

0.0386

AC XY:

26601

AN XY:

689418

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 AMR exome

AF:

0.0234

Gnomad4 ASJ exome

AF:

0.00151

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.0300

Gnomad4 NFE exome

AF:

0.0144

Gnomad4 OTH exome

AF:

0.0524

GnomAD4 genome

AF:

0.0937

AC:

14257

AN:

152190

Hom.:

1577

Cov.:

AF XY:

0.0959

AC XY:

7139

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.245

Gnomad4 AMR

AF:

0.0348

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.0275

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.0579

Alfa

AF:

0.0243

Hom.:

Bravo

AF:

0.100

TwinsUK

AF:

0.0135

AC:

ALSPAC

AF:

0.0138

AC:

ESP6500AA

AF:

0.235

AC:

325

ESP6500EA

AF:

0.0129

AC:

ExAC

AF:

0.0804

AC:

2116

Asia WGS

AF:

0.228

AC:

789

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.76

CADD

Benign

6.3

DANN

Benign

0.77

DEOGEN2

Benign

0.054

T;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.00054

LIST_S2

Benign

0.24

.;T

MetaRNN

Benign

0.0037

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-1.1

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.27

PROVEAN

Benign

0.59

N;N

REVEL

Benign

0.10

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.0050

MPC

0.34

ClinPred

0.0014

GERP RS

3.6

Varity_R

0.033

gMVP

0.029

Splicing

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