chr10-105689046-A-G

Variant names:

• chr10-105689046-A-G
• rs1833477

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 0.702 in 151,890 control chromosomes in the GnomAD database, including 37,757 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 0.70 (37757 hom., cov: 30)
• Consequence: YWHAZP5 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 1 publications found

Genes affected

YWHAZP5 (HGNC:30564): (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta pseudogene 5)

LINC02627 (HGNC:54106): (long intergenic non-protein coding RNA 2627)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836854.1. 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
	LINC02627	NR_120625.1		n.431-15358T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02627	ENST00000836854.1		n.449-15358T>C		intron	N/A
	LINC02627	ENST00000836855.1		n.395-15358T>C		intron	N/A
	LINC02627	ENST00000836856.1		n.515-15358T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106579 AN: 151772 Hom.: 37744 Cov.: 30

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.702 AC: 106647 AN: 151890 Hom.: 37757 Cov.: 30 AF XY: 0.702 AC XY: 52112 AN XY: 74248

African (AFR) AF: 0.696 AC: 28822 AN: 41404

American (AMR) AF: 0.702 AC: 10700 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2734 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4851 AN: 5164

South Asian (SAS) AF: 0.544 AC: 2619 AN: 4814

European-Finnish (FIN) AF: 0.750 AC: 7910 AN: 10544

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46759 AN: 67938

Other (OTH) AF: 0.710 AC: 1497 AN: 2108

Alfa AF: 0.671 Hom.: 15364

Bravo AF: 0.707

Asia WGS AF: 0.698 AC: 2427 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.39
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1833477; hg19: chr10-107448804;