chr10-88063390-A-G

Variant names:

• chr10-88063390-A-G
• rs945559

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 0.469 in 152,032 control chromosomes in the GnomAD database, including 18,650 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 0.47 (18650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71244 AN: 151914 Hom.: 18647 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.469 AC: 71256 AN: 152032 Hom.: 18650 Cov.: 32 AF XY: 0.471 AC XY: 35000 AN XY: 74336

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.482

Alfa AF: 0.527 Hom.: 16331

Bravo AF: 0.463

Asia WGS AF: 0.527 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.71
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs945559; hg19: chr10-89823147;