Genetic Variant NM_003458.4:c.11736G>A (chr3-49664550-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_003458.4(BSN):c.11736G>A(p.Thr3912Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 1,601,082 control chromosomes in the GnomAD database, including 68,142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 6057 hom., cov: 33)

Exomes 𝑓: 0.28 ( 62085 hom. )

Consequence

BSN
NM_003458.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.510

Variant links:

Genes affected

BSN (HGNC:1117): (bassoon presynaptic cytomatrix protein) Neurotransmitters are released from a specific site in the axon terminal called the active zone, which is composed of synaptic vesicles and a meshwork of cytoskeleton underlying the plasma membrane. The protein encoded by this gene is thought to be a scaffolding protein involved in organizing the presynaptic cytoskeleton. The gene is expressed primarily in neurons in the brain. A similar gene product in rodents is concentrated in the active zone of axon terminals and tightly associated with cytoskeletal structures, and is essential for regulating neurotransmitter release from a subset of synapses. [provided by RefSeq, Jul 2008]

BSN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 3-49664550-G-A is Benign according to our data. Variant chr3-49664550-G-A is described in ClinVar as [Benign]. Clinvar id is 3055985.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BSN	NM_003458.4 link	c.11736G>A	p.Thr3912Thr	synonymous_variant	Exon 9 of 12	ENST00000296452.5	NP_003449.2	Q9UPA5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSN	ENST00000296452.5 link	c.11736G>A	p.Thr3912Thr	synonymous_variant	Exon 9 of 12	1	NM_003458.4	ENSP00000296452.4		Q9UPA5

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40966

AN:

152072

Hom.:

6057

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.0439

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.312

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.262

AC:

62865

AN:

239664

Hom.:

9655

AF XY:

0.267

AC XY:

34454

AN XY:

129248

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.0438

Gnomad SAS exome

AF:

0.230

Gnomad FIN exome

AF:

0.445

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.284

AC:

411707

AN:

1448892

Hom.:

62085

Cov.:

AF XY:

0.283

AC XY:

203877

AN XY:

719880

show subpopulations

Gnomad4 AFR exome

AF:

0.234

Gnomad4 AMR exome

AF:

0.155

Gnomad4 ASJ exome

AF:

0.439

Gnomad4 EAS exome

AF:

0.0385

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.287

GnomAD4 genome

AF:

0.269

AC:

40981

AN:

152190

Hom.:

6057

Cov.:

AF XY:

0.272

AC XY:

20214

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.442

Gnomad4 EAS

AF:

0.0440

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.284

Hom.:

12509

Bravo

AF:

0.249

Asia WGS

AF:

0.130

AC:

456

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BSN-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

0.56

DANN

Benign

0.69

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