Genetic Variant NM_015982.4:c.169A>T (chr17-7294332-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_015982.4(YBX2):c.169A>T(p.Thr57Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,154,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T57N) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

YBX2
NM_015982.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.269

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.08574098).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YBX2	NM_015982.4	MANE Select	c.169A>T	p.Thr57Ser	missense	Exon 1 of 9	NP_057066.2	A0A384MDP4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
YBX2	ENST00000007699.10	TSL:1 MANE Select	c.169A>T	p.Thr57Ser	missense	Exon 1 of 9	ENSP00000007699.5	Q9Y2T7
YBX2	ENST00000859311.1		c.169A>T	p.Thr57Ser	missense	Exon 1 of 9	ENSP00000529370.1
YBX2	ENST00000859312.1		c.169A>T	p.Thr57Ser	missense	Exon 1 of 8	ENSP00000529371.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.000147

AC:

AN:

6808

AF XY:

0.000219

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000340

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000113

AC:

AN:

1154664

Hom.:

Cov.:

AF XY:

0.0000125

AC XY:

AN XY:

559272

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23276

American (AMR)

AF:

0.00

AC:

AN:

9330

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15216

East Asian (EAS)

AF:

0.00

AC:

AN:

26810

South Asian (SAS)

AF:

0.0000261

AC:

AN:

38308

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25404

Middle Eastern (MID)

AF:

0.000633

AC:

AN:

3162

European-Non Finnish (NFE)

AF:

0.0000103

AC:

AN:

966302

Other (OTH)

AF:

0.00

AC:

AN:

46856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.583

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Cov.:

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.00000756

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.88

DEOGEN2

Benign

0.044

Eigen

Benign

-0.52

Eigen_PC

Benign

-0.41

FATHMM_MKL

Benign

0.65

LIST_S2

Benign

0.25

M_CAP

Uncertain

0.28

MetaRNN

Benign

0.086

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.69

PhyloP100

0.27

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-0.60

REVEL

Benign

0.036

Sift

Benign

0.17

Sift4G

Benign

0.067

Polyphen

0.38

Vest4

0.24

MutPred

0.17

Gain of glycosylation at P58 (P = 0.0868)

MVP

0.043

MPC

1.2

ClinPred

0.046

GERP RS

2.4

PromoterAI

0.053

Neutral

(source)

Varity_R

0.054

gMVP

0.086

Mutation Taster

=94/6

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over