Variant 5-150618097-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001166208.2(SYNPO):c.-265-6C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 394,818 control chromosomes in the GnomAD database, including 3,378 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 2011 hom., cov: 33)

Exomes 𝑓: 0.053 ( 1367 hom. )

Consequence

SYNPO
NM_001166208.2 splice_region, intron

Scores

Splicing: ADA: 0.9992

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.42

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-150618097-C-A is Benign according to our data. Variant chr5-150618097-C-A is described in ClinVar as [Benign]. Clinvar id is 1280829.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
SYNPO	NM_001166208.2 link	c.-265-6C>A	splice_region_variant, intron_variant	NP_001159680.1	Q8N3V7-1
SYNPO	NM_001166209.2 link	c.-265-6C>A	splice_region_variant, intron_variant	NP_001159681.1	Q8N3V7-1
SYNPO	XM_006714755.4 link	c.-265-6C>A	splice_region_variant, intron_variant	XP_006714818.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNPO	ENST00000394243.5 link	c.-265-6C>A		splice_region_variant, intron_variant		1		ENSP00000377789.1		Q8N3V7-1
SYNPO	ENST00000522122.1 link	c.-265-6C>A		splice_region_variant, intron_variant		2		ENSP00000428378.1		Q8N3V7-1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15972

AN:

152076

Hom.:

2002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0393

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.0273

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0134

Gnomad OTH

AF:

0.0641

GnomAD4 exome

AF:

0.0533

AC:

12921

AN:

242624

Hom.:

1367

Cov.:

AF XY:

0.0530

AC XY:

6519

AN XY:

123102

show subpopulations

Gnomad4 AFR exome

AF:

0.286

Gnomad4 AMR exome

AF:

0.0329

Gnomad4 ASJ exome

AF:

0.00125

Gnomad4 EAS exome

AF:

0.283

Gnomad4 SAS exome

AF:

0.146

Gnomad4 FIN exome

AF:

0.0278

Gnomad4 NFE exome

AF:

0.0133

Gnomad4 OTH exome

AF:

0.0518

GnomAD4 genome

AF:

0.105

AC:

16012

AN:

152194

Hom.:

2011

Cov.:

AF XY:

0.107

AC XY:

7950

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.0393

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.171

Gnomad4 FIN

AF:

0.0273

Gnomad4 NFE

AF:

0.0134

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0206

Hom.:

Bravo

AF:

0.113

Asia WGS

AF:

0.231

AC:

800

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

BayesDel_noAF

Benign

-0.87

CADD

Benign

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.96

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