Genetic Variant NM_015982.4:c.169A>G (chr17-7294332-T-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015982.4(YBX2):c.169A>G(p.Thr57Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 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 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: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

YBX2
NM_015982.4 missense

Scores

Clinical Significance

Not reported in ClinVar

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: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.09088129).

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>G	p.Thr57Ala	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>G	p.Thr57Ala	missense	Exon 1 of 9	ENSP00000007699.5	Q9Y2T7
YBX2	ENST00000859311.1		c.169A>G	p.Thr57Ala	missense	Exon 1 of 9	ENSP00000529370.1
YBX2	ENST00000859312.1		c.169A>G	p.Thr57Ala	missense	Exon 1 of 8	ENSP00000529371.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1154662

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

559270

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:

0.00

AC:

AN:

38308

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3162

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

966300

Other (OTH)

AF:

0.00

AC:

AN:

46856

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.074

BayesDel_addAF

Benign

-0.25

BayesDel_noAF

Benign

-0.60

CADD

Benign

(source)

DANN

Benign

0.82

DEOGEN2

Benign

0.049

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.68

LIST_S2

Benign

0.25

M_CAP

Uncertain

0.25

MetaRNN

Benign

0.091

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.34

PhyloP100

0.27

PrimateAI

Pathogenic

0.90

PROVEAN

Benign

-0.34

REVEL

Benign

0.027

Sift

Benign

0.090

Sift4G

Benign

0.45

Polyphen

0.23

Vest4

0.21

MutPred

0.16

Loss of glycosylation at T57 (P = 0.0023)

MVP

0.043

MPC

1.3

ClinPred

0.12

GERP RS

2.4

PromoterAI

0.14

Neutral

(source)

Varity_R

0.057

gMVP

0.11

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over