10-81806930-C-T

Variant names:

• chr10-81806930-C-T
• rs9787485

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 0.185 in 151,870 control chromosomes in the GnomAD database, including 2,594 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 0.18 (2594 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.185 AC: 28069 AN: 151752 Hom.: 2589 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.185 AC: 28091 AN: 151870 Hom.: 2594 Cov.: 31 AF XY: 0.186 AC XY: 13806 AN XY: 74190

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.178

Alfa AF: 0.179 Hom.: 417

Bravo AF: 0.179

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9787485; hg19: chr10-83566686;