Genetic Variant UBAP2L:c.2902+1836G>C (chr1-154263533-G-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_014847.4(UBAP2L):c.2902+1836G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,012,292 control chromosomes in the GnomAD database, including 173,539 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 0.65 ( 33401 hom., cov: 32)

Exomes 𝑓: 0.57 ( 140138 hom. )

Consequence

UBAP2L
NM_014847.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38

Publications

4 publications found

Variant links:

Genes affected

UBAP2L (HGNC:29877): (ubiquitin associated protein 2 like) Enables RNA binding activity. Involved in binding activity of sperm to zona pellucida and stress granule assembly. Acts upstream of or within hematopoietic stem cell homeostasis. Part of PcG protein complex. [provided by Alliance of Genome Resources, Apr 2022]

UBAP2L Gene-Disease associations (from GenCC):

neurodevelopmental disorder with impaired language, behavioral abnormalities, and dysmorphic facies
Inheritance: AD Classification: DEFINITIVE, MODERATE Submitted by: G2P, Ambry Genetics

UBAP2L links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBAP2L	NM_014847.4 link	c.2902+1836G>C		intron_variant	Intron 24 of 26	ENST00000428931.6	NP_055662.3	Q14157-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBAP2L	ENST00000428931.6 link	c.2902+1836G>C		intron_variant	Intron 24 of 26	5	NM_014847.4	ENSP00000389445.1		Q14157-2

Frequencies

GnomAD3 genomes

AF:

0.652

AC:

99100

AN:

151966

Hom.:

33363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.780

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.554

Gnomad EAS

AF:

0.956

Gnomad SAS

AF:

0.725

Gnomad FIN

AF:

0.605

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.551

Gnomad OTH

AF:

0.645

GnomAD4 exome

AF:

0.568

AC:

488202

AN:

860208

Hom.:

140138

Cov.:

AF XY:

0.567

AC XY:

226355

AN XY:

398998

show subpopulations

African (AFR)

AF:

0.810

AC:

13502

AN:

16670

American (AMR)

AF:

0.729

AC:

1240

AN:

1702

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

3368

AN:

6194

East Asian (EAS)

AF:

0.956

AC:

4983

AN:

5212

South Asian (SAS)

AF:

0.694

AC:

12660

AN:

18250

European-Finnish (FIN)

AF:

0.573

AC:

1049

AN:

1830

Middle Eastern (MID)

AF:

0.632

AC:

1105

AN:

1748

European-Non Finnish (NFE)

AF:

0.555

AC:

432377

AN:

779460

Other (OTH)

AF:

0.615

AC:

17918

AN:

29142

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

9628

19256

28885

38513

48141

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16328

32656

48984

65312

81640

<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:

0.652

AC:

99190

AN:

152084

Hom.:

33401

Cov.:

AF XY:

0.657

AC XY:

48848

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.780

AC:

32364

AN:

41502

American (AMR)

AF:

0.701

AC:

10712

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.554

AC:

1922

AN:

3470

East Asian (EAS)

AF:

0.957

AC:

4959

AN:

5184

South Asian (SAS)

AF:

0.724

AC:

3496

AN:

4826

European-Finnish (FIN)

AF:

0.605

AC:

6383

AN:

10542

Middle Eastern (MID)

AF:

0.633

AC:

186

AN:

294

European-Non Finnish (NFE)

AF:

0.551

AC:

37434

AN:

67954

Other (OTH)

AF:

0.642

AC:

1359

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1704

3407

5111

6814

8518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.588

Hom.:

3181

Bravo

AF:

0.667

Asia WGS

AF:

0.831

AC:

2889

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

1.4

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over