9-130603440-C-G

Variant names:

• chr9-130603440-C-G
• rs7851693
• NM_003934.2:c.191-6514C>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.191-6514C>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 151,488 control chromosomes in the GnomAD database, including 8,634 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 (8634 hom., cov: 30)
• Consequence: FUBP3 NM_003934.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 28 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUBP3	NM_003934.2	MANE Select	c.191-6514C>G		intron	N/A	NP_003925.1	Q96I24-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FUBP3	ENST00000319725.10	TSL:1 MANE Select	c.191-6514C>G		intron	N/A	ENSP00000318177.9	Q96I24-1
	FUBP3	ENST00000964145.1		c.191-6514C>G		intron	N/A	ENSP00000634204.1
	FUBP3	ENST00000936135.1		c.191-6514C>G		intron	N/A	ENSP00000606194.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 49912 AN: 151378 Hom.: 8640 Cov.: 30

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.330 AC: 49932 AN: 151488 Hom.: 8634 Cov.: 30 AF XY: 0.336 AC XY: 24891 AN XY: 73972

African (AFR) AF: 0.232 AC: 9563 AN: 41264

American (AMR) AF: 0.394 AC: 5995 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1109 AN: 3466

East Asian (EAS) AF: 0.504 AC: 2579 AN: 5112

South Asian (SAS) AF: 0.287 AC: 1379 AN: 4800

European-Finnish (FIN) AF: 0.453 AC: 4705 AN: 10396

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

European-Non Finnish (NFE) AF: 0.348 AC: 23609 AN: 67922

Other (OTH) AF: 0.349 AC: 736 AN: 2106

Alfa AF: 0.192 Hom.: 392

Bravo AF: 0.325

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.63
DANN	Benign	0.67
PhyloP100		-0.69
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: rs7851693; hg19: chr9-133478827; COSMIC: COSV60513569;