rs10859032

Positions:

• chr12-90703448-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.071 in 152,162 control chromosomes in the GnomAD database, including 721 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 0.071 (721 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90703448G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02822	ENST00000652014.1	n.860+23503G>A		intron_variant
LINC02822	ENST00000664727.1	n.121+26836G>A		intron_variant
LINC02822	ENST00000666236.1	n.198+26797G>A		intron_variant
ENSG00000288102	ENST00000670607.1	n.527+54C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10794 AN: 152042 Hom.: 718 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0710 AC: 10797 AN: 152162 Hom.: 721 Cov.: 32 AF XY: 0.0746 AC XY: 5553 AN XY: 74402

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0532

Gnomad4 NFE AF: 0.0577

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0627 Hom.: 168

Bravo AF: 0.0786

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10859032; hg19: chr12-91097225;