10-105689046-A-G

Variant names:

• chr10-105689046-A-G
• rs1833477

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YWHAZP5		n.105689046A>G		intragenic_variant
LINC02627	NR_120625.1	n.431-15358T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.710

Alfa AF: 0.667 Hom.: 13321

Bravo AF: 0.707

Asia WGS AF: 0.698 AC: 2427 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833477; hg19: chr10-107448804;