Variant rs3745516 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003121.5(SPIB):c.340-120A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 1,399,826 control chromosomes in the GnomAD database, including 371,614 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.61 ( 31811 hom., cov: 31)

Exomes 𝑓: 0.73 ( 339803 hom. )

Consequence

SPIB
NM_003121.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.215

Variant links:

Genes affected

SPIB (HGNC:11242): (Spi-B transcription factor) The protein encoded by this gene is a transcriptional activator that binds to the PU-box (5'-GAGGAA-3') and acts as a lymphoid-specific enhancer. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

SPIB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SPIB	NM_003121.5 linkuse as main transcript	c.340-120A>G	intron_variant	ENST00000595883.6
SPIB	NM_001243998.2 linkuse as main transcript	c.67-120A>G	intron_variant
SPIB	NM_001243999.2 linkuse as main transcript	c.340-120A>G	intron_variant
SPIB	NM_001244000.2 linkuse as main transcript	c.282-155A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPIB	ENST00000595883.6 linkuse as main transcript	c.340-120A>G		intron_variant		1	NM_003121.5	P1	Q01892-1

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93486

AN:

151982

Hom.:

31806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.205

Gnomad SAS

AF:

0.611

Gnomad FIN

AF:

0.832

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.602

GnomAD4 exome

AF:

0.727

AC:

907238

AN:

1247724

Hom.:

339803

AF XY:

0.725

AC XY:

446919

AN XY:

616306

show subpopulations

Gnomad4 AFR exome

AF:

0.333

Gnomad4 AMR exome

AF:

0.662

Gnomad4 ASJ exome

AF:

0.656

Gnomad4 EAS exome

AF:

0.175

Gnomad4 SAS exome

AF:

0.644

Gnomad4 FIN exome

AF:

0.815

Gnomad4 NFE exome

AF:

0.768

Gnomad4 OTH exome

AF:

0.685

GnomAD4 genome

AF:

0.615

AC:

93530

AN:

152102

Hom.:

31811

Cov.:

AF XY:

0.616

AC XY:

45814

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.345

Gnomad4 AMR

AF:

0.660

Gnomad4 ASJ

AF:

0.649

Gnomad4 EAS

AF:

0.205

Gnomad4 SAS

AF:

0.610

Gnomad4 FIN

AF:

0.832

Gnomad4 NFE

AF:

0.763

Gnomad4 OTH

AF:

0.605

Alfa

AF:

0.717

Hom.:

87459

Bravo

AF:

0.588

Asia WGS

AF:

0.428

AC:

1489

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.3

DANN

Benign

0.34

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over