Genetic Variant UNC119B:p.Pro87Pro (chr12-120713290-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001080533.3(UNC119B):c.261C>T(p.Pro87Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,610,150 control chromosomes in the GnomAD database, including 4,300 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 0.10 ( 2011 hom., cov: 33)

Exomes 𝑓: 0.022 ( 2289 hom. )

Consequence

UNC119B
NM_001080533.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.14

Publications

8 publications found

Variant links:

Genes affected

UNC119B (HGNC:16488): (unc-119 lipid binding chaperone B) Enables lipid binding activity. Involved in cilium assembly and lipoprotein transport. Located in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

UNC119B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP7

Synonymous conserved (PhyloP=-3.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080533.3. 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
	UNC119B	NM_001080533.3	MANE Select	c.261C>T	p.Pro87Pro	synonymous	Exon 2 of 5	NP_001074002.1	A6NIH7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
UNC119B	ENST00000344651.5	TSL:2 MANE Select	c.261C>T	p.Pro87Pro	synonymous	Exon 2 of 5	ENSP00000344942.4	A6NIH7
UNC119B	ENST00000953441.1		c.261C>T	p.Pro87Pro	synonymous	Exon 2 of 3	ENSP00000623500.1
UNC119B	ENST00000718082.1		c.244+2572C>T		intron	N/A	ENSP00000520660.1	A0ABB0MV57

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15335

AN:

151978

Hom.:

2007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0624

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.0240

Gnomad FIN

AF:

0.0256

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.00860

Gnomad OTH

AF:

0.0662

GnomAD2 exomes

AF:

0.0502

AC:

12573

AN:

250558

AF XY:

0.0423

show subpopulations

Gnomad AFR exome

AF:

0.308

Gnomad AMR exome

AF:

0.0687

Gnomad ASJ exome

AF:

0.0162

Gnomad EAS exome

AF:

0.148

Gnomad FIN exome

AF:

0.0213

Gnomad NFE exome

AF:

0.00879

Gnomad OTH exome

AF:

0.0372

GnomAD4 exome

AF:

0.0222

AC:

32355

AN:

1458054

Hom.:

2289

Cov.:

AF XY:

0.0210

AC XY:

15253

AN XY:

725252

show subpopulations

African (AFR)

AF:

0.311

AC:

10373

AN:

33324

American (AMR)

AF:

0.0683

AC:

3041

AN:

44498

Ashkenazi Jewish (ASJ)

AF:

0.0157

AC:

410

AN:

26052

East Asian (EAS)

AF:

0.131

AC:

5203

AN:

39636

South Asian (SAS)

AF:

0.0231

AC:

1989

AN:

86030

European-Finnish (FIN)

AF:

0.0194

AC:

1037

AN:

53346

Middle Eastern (MID)

AF:

0.0417

AC:

240

AN:

5756

European-Non Finnish (NFE)

AF:

0.00701

AC:

7770

AN:

1109198

Other (OTH)

AF:

0.0381

AC:

2292

AN:

60214

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

1225

2450

3675

4900

6125

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

578

1156

1734

2312

2890

<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

AF:

0.101

AC:

15363

AN:

152096

Hom.:

2011

Cov.:

AF XY:

0.100

AC XY:

7449

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.301

AC:

12471

AN:

41452

American (AMR)

AF:

0.0625

AC:

955

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0170

AC:

AN:

3468

East Asian (EAS)

AF:

0.144

AC:

747

AN:

5182

South Asian (SAS)

AF:

0.0243

AC:

117

AN:

4820

European-Finnish (FIN)

AF:

0.0256

AC:

271

AN:

10580

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00860

AC:

585

AN:

68014

Other (OTH)

AF:

0.0665

AC:

140

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

594

1188

1783

2377

2971

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0398

Hom.:

1285

Bravo

AF:

0.115

Asia WGS

AF:

0.0980

AC:

341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

1.2

(source)

DANN

Benign

0.60

PhyloP100

-3.1

Mutation Taster

=100/0

polymorphism (auto)

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over