dbSNP rs953432114: FUBP3:p.Asp21Asn (chr9-130579741-G-A) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 1P and 4B. PP3BS2

The NM_003934.2(FUBP3):c.61G>A(p.Asp21Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000159 in 1,129,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

FUBP3
NM_003934.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.38

Publications

0 publications found

Variant links:

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]

FUBP3 links:

LOC100272217 (HGNC:):

LOC100272217 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.813

BS2

High AC in GnomAdExome4 at 18 AD gene.

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.61G>A	p.Asp21Asn	missense	Exon 1 of 19	NP_003925.1	Q96I24-1
	LOC100272217	NR_027440.1		n.-247C>T		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FUBP3	ENST00000319725.10	TSL:1 MANE Select	c.61G>A	p.Asp21Asn	missense	Exon 1 of 19	ENSP00000318177.9	Q96I24-1
FUBP3	ENST00000964145.1		c.61G>A	p.Asp21Asn	missense	Exon 1 of 21	ENSP00000634204.1
FUBP3	ENST00000936135.1		c.61G>A	p.Asp21Asn	missense	Exon 1 of 19	ENSP00000606194.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000154

AC:

AN:

64940

AF XY:

0.0000274

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000274

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000159

AC:

AN:

1129066

Hom.:

Cov.:

AF XY:

0.0000112

AC XY:

AN XY:

537868

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24500

American (AMR)

AF:

0.00

AC:

AN:

14100

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14796

East Asian (EAS)

AF:

0.00

AC:

AN:

29352

South Asian (SAS)

AF:

0.0000877

AC:

AN:

22812

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32144

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3298

European-Non Finnish (NFE)

AF:

0.0000170

AC:

AN:

942844

Other (OTH)

AF:

0.00

AC:

AN:

45220

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.80

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.40

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.24

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.53

FATHMM_MKL

Benign

0.55

LIST_S2

Uncertain

0.94

M_CAP

Pathogenic

0.69

MetaRNN

Pathogenic

0.81

MetaSVM

Benign

-0.41

MutationAssessor

Uncertain

2.6

PhyloP100

4.4

PrimateAI

Pathogenic

0.90

PROVEAN

Uncertain

-3.0

REVEL

Benign

0.23

Sift

Benign

0.059

Sift4G

Uncertain

0.031

Polyphen

1.0

Vest4

0.53

MutPred

0.42

Gain of MoRF binding (P = 0.0312)

MVP

0.73

MPC

0.57

ClinPred

0.78

GERP RS

4.2

PromoterAI

0.011

Neutral

(source)

Varity_R

0.42

gMVP

0.62

Mutation Taster

=92/8

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over