Genetic Variant YJU2B:c.573+67C>A (chr19-13759339-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_030818.4(YJU2B):c.573+67C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 1,320,870 control chromosomes in the GnomAD database, including 145,095 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 0.53 ( 22593 hom., cov: 32)

Exomes 𝑓: 0.45 ( 122502 hom. )

Consequence

YJU2B
NM_030818.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.50

Publications

38 publications found

Variant links:

Genes affected

YJU2B (HGNC:28118): (YJU2 splicing factor homolog B) Involved in response to virus. Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

YJU2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YJU2B	NM_030818.4 link	c.573+67C>A		intron_variant	Intron 8 of 9	ENST00000221554.13	NP_110445.1	P13994

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YJU2B	ENST00000221554.13 link	c.573+67C>A		intron_variant	Intron 8 of 9	1	NM_030818.4	ENSP00000221554.7		P13994

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80229

AN:

151840

Hom.:

22544

Cov.:

show subpopulations

Gnomad AFR

AF:

0.742

Gnomad AMI

AF:

0.568

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.411

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.481

GnomAD2 exomes

AF:

0.493

AC:

47391

AN:

96050

AF XY:

0.491

show subpopulations

Gnomad AFR exome

AF:

0.759

Gnomad AMR exome

AF:

0.436

Gnomad ASJ exome

AF:

0.494

Gnomad EAS exome

AF:

0.607

Gnomad FIN exome

AF:

0.452

Gnomad NFE exome

AF:

0.440

Gnomad OTH exome

AF:

0.450

GnomAD4 exome

AF:

0.452

AC:

528779

AN:

1168912

Hom.:

122502

Cov.:

AF XY:

0.453

AC XY:

261302

AN XY:

576412

show subpopulations

African (AFR)

AF:

0.748

AC:

19829

AN:

26506

American (AMR)

AF:

0.425

AC:

10824

AN:

25450

Ashkenazi Jewish (ASJ)

AF:

0.472

AC:

9278

AN:

19640

East Asian (EAS)

AF:

0.608

AC:

21026

AN:

34610

South Asian (SAS)

AF:

0.517

AC:

33656

AN:

65052

European-Finnish (FIN)

AF:

0.454

AC:

20563

AN:

45258

Middle Eastern (MID)

AF:

0.421

AC:

1577

AN:

3746

European-Non Finnish (NFE)

AF:

0.433

AC:

388942

AN:

899046

Other (OTH)

AF:

0.465

AC:

23084

AN:

49604

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

14800

29601

44401

59202

74002

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11782

23564

35346

47128

58910

<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:

0.529

AC:

80342

AN:

151958

Hom.:

22593

Cov.:

AF XY:

0.526

AC XY:

39097

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.742

AC:

30785

AN:

41480

American (AMR)

AF:

0.423

AC:

6462

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

1624

AN:

3460

East Asian (EAS)

AF:

0.611

AC:

3140

AN:

5142

South Asian (SAS)

AF:

0.517

AC:

2492

AN:

4822

European-Finnish (FIN)

AF:

0.447

AC:

4714

AN:

10542

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.434

AC:

29462

AN:

67930

Other (OTH)

AF:

0.484

AC:

1021

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1842

3685

5527

7370

9212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.468

Hom.:

40057

Bravo

AF:

0.536

Asia WGS

AF:

0.597

AC:

2074

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.0010

(source)

DANN

Benign

0.44

PhyloP100

-6.5

PromoterAI

-0.059

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over