dbSNP rs371671: 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:

Genome browser will be placed here

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030818.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
YJU2B	NM_030818.4	MANE Select	c.573+67C>A	intron	N/A	NP_110445.1	P13994
YJU2B	NM_001320561.2		c.573+67C>A	intron	N/A	NP_001307490.1	P13994
YJU2B	NM_001320564.2		c.573+67C>A	intron	N/A	NP_001307493.1	P13994

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
YJU2B	ENST00000221554.13	TSL:1 MANE Select	c.573+67C>A		intron	N/A	ENSP00000221554.7	P13994
YJU2B	ENST00000588809.1	TSL:3	c.554C>A	p.Pro185His	missense	Exon 5 of 5	ENSP00000465392.1	K7EJZ6
YJU2B	ENST00000589096.1	TSL:6	c.*249C>A		3_prime_UTR	Exon 1 of 1	ENSP00000467202.1	K7EP29

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over