rs3744404

chr17-7289873-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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]

ACMG classification

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	UniProt
YBX2	NM_015982.4	c.848+95G>A		intron_variant		ENST00000007699.10
YBX2	XM_017024713.3	c.893+95G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0364 AC: 5541 AN: 152216 Hom.: 314 Cov.: 34

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.: 32 AF XY: 0.0315 AC XY: 22387 AN XY: 711278

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.: 34 AF XY: 0.0393 AC XY: 2925 AN XY: 74492

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.: 82

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

Other links and lift over

dbSNP: rs3744404; hg19: chr17-7193192; COSMIC: COSV50302268; COSMIC: COSV50302268;