dbSNP rs3744404: YBX2:c.848+95G>A (chr17-7289873-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015982.4(YBX2):c.848+95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 1,586,334 control chromosomes in the GnomAD database, including 2,745 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 0.036 ( 317 hom., cov: 34)

Exomes 𝑓: 0.031 ( 2428 hom. )

Consequence

YBX2
NM_015982.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133

Publications

3 publications found

Variant links:

Genes affected

YBX2 (HGNC:17948): (Y-box binding protein 2) This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]

YBX2 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=-0.74).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YBX2	NM_015982.4 link	c.848+95G>A		intron_variant	Intron 6 of 8	ENST00000007699.10	NP_057066.2
YBX2	XM_017024713.3 link	c.893+95G>A		intron_variant	Intron 7 of 9		XP_016880202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YBX2	ENST00000007699.10 link	c.848+95G>A		intron_variant	Intron 6 of 8	1	NM_015982.4	ENSP00000007699.5

Frequencies

GnomAD3 genomes

AF:

0.0364

AC:

5541

AN:

152216

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0525

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.0718

Gnomad FIN

AF:

0.0339

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0184

Gnomad OTH

AF:

0.0411

GnomAD4 exome

AF:

0.0311

AC:

44635

AN:

1434000

Hom.:

2428

Cov.:

AF XY:

0.0315

AC XY:

22387

AN XY:

711278

show subpopulations

African (AFR)

AF:

0.0229

AC:

755

AN:

32904

American (AMR)

AF:

0.0636

AC:

2735

AN:

42982

Ashkenazi Jewish (ASJ)

AF:

0.0599

AC:

1478

AN:

24658

East Asian (EAS)

AF:

0.296

AC:

11619

AN:

39230

South Asian (SAS)

AF:

0.0596

AC:

4989

AN:

83670

European-Finnish (FIN)

AF:

0.0281

AC:

1466

AN:

52112

Middle Eastern (MID)

AF:

0.0334

AC:

162

AN:

4852

European-Non Finnish (NFE)

AF:

0.0171

AC:

18723

AN:

1094532

Other (OTH)

AF:

0.0459

AC:

2708

AN:

59060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

2275

4551

6826

9102

11377

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

954

1908

2862

3816

4770

<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:

0.0364

AC:

5545

AN:

152334

Hom.:

317

Cov.:

AF XY:

0.0393

AC XY:

2925

AN XY:

74492

show subpopulations

African (AFR)

AF:

0.0240

AC:

997

AN:

41578

American (AMR)

AF:

0.0526

AC:

806

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

211

AN:

3472

East Asian (EAS)

AF:

0.285

AC:

1474

AN:

5172

South Asian (SAS)

AF:

0.0706

AC:

341

AN:

4830

European-Finnish (FIN)

AF:

0.0339

AC:

360

AN:

10626

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0184

AC:

1252

AN:

68024

Other (OTH)

AF:

0.0440

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

255

510

765

1020

1275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0281

Hom.:

249

Bravo

AF:

0.0396

Asia WGS

AF:

0.178

AC:

620

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

1.3

(source)

DANN

Benign

0.79

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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