Variant 5-176620760-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 NM_003085.5(SNCB):c.*51C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 1,348,262 control chromosomes in the GnomAD database, including 10,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.083 ( 1031 hom., cov: 32)

Exomes 𝑓: 0.094 ( 9409 hom. )

Consequence

SNCB
NM_003085.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.50

Variant links:

Genes affected

SNCB (HGNC:11140): (synuclein beta) This gene encodes a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals with dementia with Lewy bodies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

SNCB 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 (BayesDel_noAF=-0.58).

BP6

Variant 5-176620760-G-A is Benign according to our data. Variant chr5-176620760-G-A is described in ClinVar as [Benign]. Clinvar id is 1222753.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNCB	NM_003085.5 linkuse as main transcript	c.*51C>T		3_prime_UTR_variant	6/6	ENST00000393693.7	NP_003076.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNCB	ENST00000393693.7 linkuse as main transcript	c.*51C>T		3_prime_UTR_variant	6/6	1	NM_003085.5	ENSP00000377296	P1

Frequencies

GnomAD3 genomes

AF:

0.0828

AC:

12591

AN:

152056

Hom.:

1020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0391

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0584

Gnomad OTH

AF:

0.0913

GnomAD3 exomes

AF:

0.125

AC:

31388

AN:

250312

Hom.:

3664

AF XY:

0.121

AC XY:

16419

AN XY:

135618

show subpopulations

Gnomad AFR exome

AF:

0.0394

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.0517

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.0594

Gnomad OTH exome

AF:

0.106

GnomAD4 exome

AF:

0.0939

AC:

112360

AN:

1196088

Hom.:

9409

Cov.:

AF XY:

0.0938

AC XY:

57003

AN XY:

607656

show subpopulations

Gnomad4 AFR exome

AF:

0.0402

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.0532

Gnomad4 EAS exome

AF:

0.480

Gnomad4 SAS exome

AF:

0.148

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.0670

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.0829

AC:

12610

AN:

152174

Hom.:

1031

Cov.:

AF XY:

0.0903

AC XY:

6719

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0391

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.0522

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.0584

Gnomad4 OTH

AF:

0.0989

Alfa

AF:

0.0663

Hom.:

393

Bravo

AF:

0.0843

Asia WGS

AF:

0.325

AC:

1126

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 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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