Variant 5-176626621-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.163+99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0831 in 1,528,242 control chromosomes in the GnomAD database, including 9,954 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.086 ( 1018 hom., cov: 32)

Exomes 𝑓: 0.083 ( 8936 hom. )

Consequence

SNCB
NM_003085.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.08

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:

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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=-0.9).

BP6

Variant 5-176626621-G-A is Benign according to our data. Variant chr5-176626621-G-A is described in ClinVar as [Benign]. Clinvar id is 1267656.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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+99C>T		intron_variant		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.163+99C>T		intron_variant		1	NM_003085.5	ENSP00000377296	P1

Frequencies

GnomAD3 genomes

AF:

0.0861

AC:

13085

AN:

151966

Hom.:

1007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0523

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.441

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0585

Gnomad OTH

AF:

0.0950

GnomAD3 exomes

AF:

0.125

AC:

31193

AN:

249162

Hom.:

3518

AF XY:

0.121

AC XY:

16325

AN XY:

134890

show subpopulations

Gnomad AFR exome

AF:

0.0518

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.0518

Gnomad EAS exome

AF:

0.465

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.130

Gnomad NFE exome

AF:

0.0593

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.0827

AC:

113840

AN:

1376158

Hom.:

8936

Cov.:

AF XY:

0.0837

AC XY:

57731

AN XY:

689616

show subpopulations

Gnomad4 AFR exome

AF:

0.0497

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.0513

Gnomad4 EAS exome

AF:

0.464

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.0576

Gnomad4 OTH exome

AF:

0.0979

GnomAD4 genome

AF:

0.0862

AC:

13105

AN:

152084

Hom.:

1018

Cov.:

AF XY:

0.0933

AC XY:

6932

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.0523

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0522

Gnomad4 EAS

AF:

0.441

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.0585

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0663

Hom.:

Bravo

AF:

0.0885

Asia WGS

AF:

0.320

AC:

1107

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

-0.90

CADD

Benign

0.28

DANN

Benign

0.57

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