Variant rs1543116 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198925.4(SEMA4B):c.322-8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 1,610,618 control chromosomes in the GnomAD database, including 100,207 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 12101 hom., cov: 31)

Exomes 𝑓: 0.34 ( 88106 hom. )

Consequence

SEMA4B
NM_198925.4 splice_region, intron

Scores

Splicing: ADA: 0.00001581

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.800

Variant links:

Genes affected

SEMA4B (HGNC:10730): (semaphorin 4B) Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in plasma membrane. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SEMA4B links:

SEMA4B (HGNC:):

SEMA4B 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA4B	NM_198925.4 linkuse as main transcript	c.322-8T>C		splice_region_variant, intron_variant		ENST00000411539.7	NP_945119.1	Q9NPR2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA4B	ENST00000411539.7 linkuse as main transcript	c.322-8T>C		splice_region_variant, intron_variant		1	NM_198925.4	ENSP00000394720.2		Q9NPR2-1

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59319

AN:

151760

Hom.:

12085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.392

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.370

GnomAD3 exomes

AF:

0.335

AC:

82621

AN:

246296

Hom.:

14450

AF XY:

0.331

AC XY:

44170

AN XY:

133590

show subpopulations

Gnomad AFR exome

AF:

0.501

Gnomad AMR exome

AF:

0.308

Gnomad ASJ exome

AF:

0.380

Gnomad EAS exome

AF:

0.189

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.427

Gnomad NFE exome

AF:

0.349

Gnomad OTH exome

AF:

0.342

GnomAD4 exome

AF:

0.344

AC:

501776

AN:

1458740

Hom.:

88106

Cov.:

AF XY:

0.341

AC XY:

247496

AN XY:

725570

show subpopulations

Gnomad4 AFR exome

AF:

0.511

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.383

Gnomad4 EAS exome

AF:

0.214

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.423

Gnomad4 NFE exome

AF:

0.348

Gnomad4 OTH exome

AF:

0.347

GnomAD4 genome

AF:

0.391

AC:

59361

AN:

151878

Hom.:

12101

Cov.:

AF XY:

0.389

AC XY:

28895

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.499

Gnomad4 AMR

AF:

0.337

Gnomad4 ASJ

AF:

0.392

Gnomad4 EAS

AF:

0.196

Gnomad4 SAS

AF:

0.238

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.358

Gnomad4 OTH

AF:

0.374

Alfa

AF:

0.358

Hom.:

16245

Bravo

AF:

0.390

Asia WGS

AF:

0.260

AC:

905

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.2

DANN

Benign

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000016

dbscSNV1_RF

Benign

0.0020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over