Genetic Variant 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:

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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=-0.74).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015982.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YBX2	NM_015982.4	MANE Select	c.848+95G>A		intron	N/A	NP_057066.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
YBX2	ENST00000007699.10	TSL:1 MANE Select	c.848+95G>A	intron	N/A	ENSP00000007699.5
YBX2	ENST00000571464.1	TSL:5	c.245+95G>A	intron	N/A	ENSP00000459587.1
YBX2	ENST00000570720.1	TSL:2	n.417+95G>A	intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over