9-130588697-A-G

Position:

• chr9-130588697-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FUBP3	NM_003934.2	c.85-6786A>G		intron_variant		ENST00000319725.10	NP_003925.1
FUBP3	XM_005272232.3	c.85-6786A>G		intron_variant			XP_005272289.1
FUBP3	XM_011519172.4	c.85-6786A>G		intron_variant			XP_011517474.1
FUBP3	XR_007061369.1	n.189-6786A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FUBP3	ENST00000319725.10	c.85-6786A>G		intron_variant		1	NM_003934.2	ENSP00000318177	P1
FUBP3	ENST00000650723.1	c.*805-6786A>G		intron_variant, NMD_transcript_variant				ENSP00000499109
FUBP3	ENST00000699747.1	c.85-6786A>G		intron_variant, NMD_transcript_variant				ENSP00000514557
FUBP3	ENST00000465949.1	n.420-6786A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.348

Alfa AF: 0.349 Hom.: 14739

Bravo AF: 0.325

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.16
DANN	Benign	0.57

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: rs7466269; hg19: chr9-133464084;