12-10711605-C-T

Variant names:

• chr12-10711605-C-T
• rs797172
• NM_003651.5:c.574-1491G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003651.5(YBX3):​c.574-1491G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,094 control chromosomes in the GnomAD database, including 5,923 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 0.27 (5923 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: YBX3 NM_003651.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 8 publications found

Genes affected

YBX3 (HGNC:2428): (Y-box binding protein 3) Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003651.5. 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
	YBX3	NM_003651.5	MANE Select	c.574-1491G>A		intron	N/A	NP_003642.3
	YBX3	NM_001145426.2		c.573+1606G>A		intron	N/A	NP_001138898.1	P16989-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YBX3	ENST00000228251.9	TSL:1 MANE Select	c.574-1491G>A		intron	N/A	ENSP00000228251.4	P16989-1
	YBX3	ENST00000279550.11	TSL:1	c.573+1606G>A		intron	N/A	ENSP00000279550.7	P16989-2
	YBX3	ENST00000955210.1		c.574-1491G>A		intron	N/A	ENSP00000625269.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40844 AN: 151976 Hom.: 5918 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.275

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.269 AC: 40863 AN: 152094 Hom.: 5923 Cov.: 33 AF XY: 0.276 AC XY: 20519 AN XY: 74362

African (AFR) AF: 0.175 AC: 7244 AN: 41498

American (AMR) AF: 0.300 AC: 4586 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1355 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1313 AN: 5182

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4822

European-Finnish (FIN) AF: 0.366 AC: 3862 AN: 10558

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19632 AN: 67966

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.276 Hom.: 4242

Bravo AF: 0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.61
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs797172; hg19: chr12-10864204;