chr9-130588697-A-G

Variant names:

• chr9-130588697-A-G
• rs7466269
• NM_003934.2:c.85-6786A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003934.2(FUBP3):​c.85-6786A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,072 control chromosomes in the GnomAD database, including 8,681 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 0.33 (8681 hom., cov: 32)
• Consequence: FUBP3 NM_003934.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901
• Publications: 62 publications found

Genes affected

FUBP3 (HGNC:4005): (far upstream element binding protein 3) Enables single-stranded DNA binding activity. Involved in positive regulation of gene expression; positive regulation of transcription, DNA-templated; and transcription, DNA-templated. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003934.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUBP3	NM_003934.2	MANE Select	c.85-6786A>G		intron	N/A	NP_003925.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUBP3	ENST00000319725.10	TSL:1 MANE Select	c.85-6786A>G		intron	N/A	ENSP00000318177.9
	FUBP3	ENST00000465949.1	TSL:5	n.420-6786A>G		intron	N/A
	FUBP3	ENST00000650723.1		n.*805-6786A>G		intron	N/A	ENSP00000499109.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50176 AN: 151954 Hom.: 8687 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50196 AN: 152072 Hom.: 8681 Cov.: 32 AF XY: 0.337 AC XY: 25073 AN XY: 74326

African (AFR) AF: 0.233 AC: 9665 AN: 41514

American (AMR) AF: 0.394 AC: 6012 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2596 AN: 5164

South Asian (SAS) AF: 0.288 AC: 1390 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4792 AN: 10566

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23637 AN: 67956

Other (OTH) AF: 0.348 AC: 735 AN: 2110

Alfa AF: 0.345 Hom.: 32940

Bravo AF: 0.325

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.57
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7466269; hg19: chr9-133464084; COSMIC: COSV107325420;