5-72418500-C-T

Variant names:

• chr5-72418500-C-T
• rs6886010

Variant summary

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

The variant allele was found at a frequency of 0.479 in 151,912 control chromosomes in the GnomAD database, including 17,872 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 0.48 (17872 hom., cov: 31)
• Consequence: YBX1P5 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 1 publications found

Genes affected

YBX1P5 (HGNC:42426): (Y-box binding protein 1 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509441.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YBX1P5	ENST00000509441.1	TSL:6	n.*165C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72748 AN: 151794 Hom.: 17861 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.484

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.479 AC: 72812 AN: 151912 Hom.: 17872 Cov.: 31 AF XY: 0.484 AC XY: 35944 AN XY: 74228

African (AFR) AF: 0.468 AC: 19389 AN: 41396

American (AMR) AF: 0.479 AC: 7309 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1442 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4515 AN: 5164

South Asian (SAS) AF: 0.523 AC: 2526 AN: 4828

European-Finnish (FIN) AF: 0.519 AC: 5478 AN: 10546

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30659 AN: 67940

Other (OTH) AF: 0.487 AC: 1024 AN: 2102

Alfa AF: 0.435 Hom.: 5088

Bravo AF: 0.479

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.62
PhyloP100		1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6886010; hg19: chr5-71714327;