Variant 5-176626644-C-G 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.163+76G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,566,228 control chromosomes in the GnomAD database, including 167,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.35 ( 11698 hom., cov: 32)

Exomes 𝑓: 0.45 ( 155943 hom. )

Consequence

SNCB
NM_003085.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.12

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:

SNCB (HGNC:):

SNCB links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 5-176626644-C-G is Benign according to our data. Variant chr5-176626644-C-G is described in ClinVar as [Benign]. Clinvar id is 1257127.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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.163+76G>C		intron_variant		ENST00000393693.7	NP_003076.1	Q16143

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNCB	ENST00000393693.7 linkuse as main transcript	c.163+76G>C		intron_variant		1	NM_003085.5	ENSP00000377296.2		Q16143

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53012

AN:

151884

Hom.:

11691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.404

Gnomad EAS

AF:

0.0202

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.484

Gnomad OTH

AF:

0.375

GnomAD3 exomes

AF:

0.386

AC:

96441

AN:

250152

Hom.:

21461

AF XY:

0.387

AC XY:

52339

AN XY:

135398

show subpopulations

Gnomad AFR exome

AF:

0.100

Gnomad AMR exome

AF:

0.459

Gnomad ASJ exome

AF:

0.391

Gnomad EAS exome

AF:

0.0115

Gnomad SAS exome

AF:

0.259

Gnomad FIN exome

AF:

0.464

Gnomad NFE exome

AF:

0.482

Gnomad OTH exome

AF:

0.421

GnomAD4 exome

AF:

0.454

AC:

641567

AN:

1414226

Hom.:

155943

Cov.:

AF XY:

0.449

AC XY:

317217

AN XY:

706440

show subpopulations

Gnomad4 AFR exome

AF:

0.0904

Gnomad4 AMR exome

AF:

0.458

Gnomad4 ASJ exome

AF:

0.400

Gnomad4 EAS exome

AF:

0.0268

Gnomad4 SAS exome

AF:

0.266

Gnomad4 FIN exome

AF:

0.467

Gnomad4 NFE exome

AF:

0.499

Gnomad4 OTH exome

AF:

0.411

GnomAD4 genome

AF:

0.349

AC:

53021

AN:

152002

Hom.:

11698

Cov.:

AF XY:

0.344

AC XY:

25564

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.404

Gnomad4 EAS

AF:

0.0201

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.463

Gnomad4 NFE

AF:

0.484

Gnomad4 OTH

AF:

0.371

Alfa

AF:

0.332

Hom.:

1554

Bravo

AF:

0.337

Asia WGS

AF:

0.130

AC:

454

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

-0.67

CADD

Benign

0.80

DANN

Benign

0.85

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