rs10763588

Variant names:

• chr10-46056060-C-A
• rs10763588

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 0.454 in 151,962 control chromosomes in the GnomAD database, including 17,380 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 0.45 (17380 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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: 0.455 AC: 69072 AN: 151844 Hom.: 17387 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.454 AC: 69064 AN: 151962 Hom.: 17380 Cov.: 31 AF XY: 0.456 AC XY: 33878 AN XY: 74270

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.456

Alfa AF: 0.527 Hom.: 7986

Bravo AF: 0.445

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10763588; hg19: chr10-51539762;