rs2066167

Variant names:

• chr10-80322584-T-C
• rs2066167

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 0.0631 in 152,282 control chromosomes in the GnomAD database, including 378 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 0.063 (378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 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: 0.0632 AC: 9612 AN: 152162 Hom.: 377 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0631 AC: 9614 AN: 152282 Hom.: 378 Cov.: 32 AF XY: 0.0627 AC XY: 4670 AN XY: 74464

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0425

Gnomad4 FIN AF: 0.0612

Gnomad4 NFE AF: 0.0575

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0596 Hom.: 256

Bravo AF: 0.0620

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066167; hg19: chr10-82082340;