rs12766391

Variant names:

• chr10-62681444-G-A
• rs12766391

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 0.307 in 152,020 control chromosomes in the GnomAD database, including 8,525 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 0.31 (8525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 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: 0.308 AC: 46760 AN: 151912 Hom.: 8529 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.307 AC: 46740 AN: 152020 Hom.: 8525 Cov.: 32 AF XY: 0.309 AC XY: 22954 AN XY: 74282

African (AFR) AF: 0.117 AC: 4863 AN: 41468

American (AMR) AF: 0.248 AC: 3797 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1463 AN: 3472

East Asian (EAS) AF: 0.540 AC: 2796 AN: 5176

South Asian (SAS) AF: 0.377 AC: 1813 AN: 4814

European-Finnish (FIN) AF: 0.405 AC: 4268 AN: 10526

Middle Eastern (MID) AF: 0.333 AC: 96 AN: 288

European-Non Finnish (NFE) AF: 0.391 AC: 26600 AN: 67956

Other (OTH) AF: 0.305 AC: 645 AN: 2116

Alfa AF: 0.353 Hom.: 16487

Bravo AF: 0.288

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs12766391; hg19: chr10-64441204;