Variant rs3744404 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
YBX2	NM_015982.4 linkuse as main transcript	c.848+95G>A		intron_variant		ENST00000007699.10	NP_057066.2
YBX2	XM_017024713.3 linkuse as main transcript	c.893+95G>A		intron_variant			XP_016880202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
YBX2	ENST00000007699.10 linkuse as main transcript	c.848+95G>A		intron_variant		1	NM_015982.4	ENSP00000007699	P1

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

Gnomad4 AFR exome

AF:

0.0229

Gnomad4 AMR exome

AF:

0.0636

Gnomad4 ASJ exome

AF:

0.0599

Gnomad4 EAS exome

AF:

0.296

Gnomad4 SAS exome

AF:

0.0596

Gnomad4 FIN exome

AF:

0.0281

Gnomad4 NFE exome

AF:

0.0171

Gnomad4 OTH exome

AF:

0.0459

GnomAD4 genome

AF:

0.0364

AC:

5545

AN:

152334

Hom.:

317

Cov.:

AF XY:

0.0393

AC XY:

2925

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.0240

Gnomad4 AMR

AF:

0.0526

Gnomad4 ASJ

AF:

0.0608

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.0706

Gnomad4 FIN

AF:

0.0339

Gnomad4 NFE

AF:

0.0184

Gnomad4 OTH

AF:

0.0440

Alfa

AF:

0.0233

Hom.:

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

DANN

Benign

0.79

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over