rs2066167

Variant names:

• chr10-80322584-T-C
• rs2066167

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0795 AC: 3300 AN: 41532

American (AMR) AF: 0.0603 AC: 922 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5194

South Asian (SAS) AF: 0.0425 AC: 205 AN: 4822

European-Finnish (FIN) AF: 0.0612 AC: 650 AN: 10616

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0575 AC: 3914 AN: 68030

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0603 Hom.: 352

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
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs2066167; hg19: chr10-82082340;