rs62116061

chr19-50422187-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003121.5(SPIB):c.52-286T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,128 control chromosomes in the GnomAD database, including 31,680 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 (31680 hom., cov: 34)
• Consequence: SPIB NM_003121.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPIB	NM_003121.5	c.52-286T>G		intron_variant		ENST00000595883.6
SPIB	NM_001243998.2	c.-7-286T>G		intron_variant
SPIB	NM_001243999.2	c.52-286T>G		intron_variant
SPIB	NM_001244000.2	c.-7-286T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPIB	ENST00000595883.6	c.52-286T>G		intron_variant		1	NM_003121.5	P1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93154 AN: 152010 Hom.: 31680 Cov.: 34

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.600

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.613 AC: 93193 AN: 152128 Hom.: 31680 Cov.: 34 AF XY: 0.614 AC XY: 45682 AN XY: 74368

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.604

Alfa AF: 0.677 Hom.: 4570

Bravo AF: 0.585

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs62116061; hg19: chr19-50925444;