Variant rs222859 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000007699.10(YBX2):c.26G>T(p.Gly9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 1,471,966 control chromosomes in the GnomAD database, including 461,692 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.80 ( 48202 hom., cov: 33)

Exomes 𝑓: 0.79 ( 413490 hom. )

Consequence

YBX2
ENST00000007699.10 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.593

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 (MetaRNN=7.9461034E-7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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.26G>T	p.Gly9Val	missense_variant	1/9	ENST00000007699.10	NP_057066.2
YBX2	XM_017024713.3 linkuse as main transcript	c.26G>T	p.Gly9Val	missense_variant	1/10		XP_016880202.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
YBX2	ENST00000007699.10 linkuse as main transcript	c.26G>T	p.Gly9Val	missense_variant	1/9	1	NM_015982.4	ENSP00000007699	P1
YBX2	ENST00000571127.1 linkuse as main transcript	n.82G>T		non_coding_transcript_exon_variant	1/2	2
YBX2	ENST00000571485.5 linkuse as main transcript	n.115G>T		non_coding_transcript_exon_variant	1/6	2
YBX2	ENST00000570627.1 linkuse as main transcript	n.48+93G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.797

AC:

120305

AN:

151030

Hom.:

48138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.836

Gnomad AMI

AF:

0.871

Gnomad AMR

AF:

0.728

Gnomad ASJ

AF:

0.750

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.824

Gnomad MID

AF:

0.833

Gnomad NFE

AF:

0.807

Gnomad OTH

AF:

0.801

GnomAD3 exomes

AF:

0.725

AC:

64248

AN:

88634

Hom.:

23871

AF XY:

0.727

AC XY:

36387

AN XY:

50060

show subpopulations

Gnomad AFR exome

AF:

0.844

Gnomad AMR exome

AF:

0.615

Gnomad ASJ exome

AF:

0.756

Gnomad EAS exome

AF:

0.641

Gnomad SAS exome

AF:

0.657

Gnomad FIN exome

AF:

0.821

Gnomad NFE exome

AF:

0.811

Gnomad OTH exome

AF:

0.776

GnomAD4 exome

AF:

0.789

AC:

1042475

AN:

1320828

Hom.:

413490

Cov.:

AF XY:

0.785

AC XY:

511802

AN XY:

651606

show subpopulations

Gnomad4 AFR exome

AF:

0.838

Gnomad4 AMR exome

AF:

0.643

Gnomad4 ASJ exome

AF:

0.758

Gnomad4 EAS exome

AF:

0.675

Gnomad4 SAS exome

AF:

0.653

Gnomad4 FIN exome

AF:

0.823

Gnomad4 NFE exome

AF:

0.805

Gnomad4 OTH exome

AF:

0.779

GnomAD4 genome

AF:

0.797

AC:

120424

AN:

151138

Hom.:

48202

Cov.:

AF XY:

0.794

AC XY:

58614

AN XY:

73816

show subpopulations

Gnomad4 AFR

AF:

0.836

Gnomad4 AMR

AF:

0.728

Gnomad4 ASJ

AF:

0.750

Gnomad4 EAS

AF:

0.643

Gnomad4 SAS

AF:

0.650

Gnomad4 FIN

AF:

0.824

Gnomad4 NFE

AF:

0.807

Gnomad4 OTH

AF:

0.804

Alfa

AF:

0.799

Hom.:

10313

Bravo

AF:

0.793

TwinsUK

AF:

0.810

AC:

3003

ALSPAC

AF:

0.807

AC:

3109

ExAC

AF:

0.616

AC:

8274

Asia WGS

AF:

0.689

AC:

2181

AN:

3164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.046

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.94

DEOGEN2

Benign

0.037

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.085

LIST_S2

Benign

0.24

MetaRNN

Benign

7.9e-7

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

MutationTaster

Benign

0.61

PrimateAI

Pathogenic

0.89

PROVEAN

Benign

-0.41

REVEL

Benign

0.063

Sift

Benign

0.24

Sift4G

Benign

0.43

Polyphen

0.0

Vest4

0.064

MPC

1.6

ClinPred

0.0052

GERP RS

2.6

Varity_R

0.050

gMVP

0.11

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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