rs1566667

Variant names:

• chr12-130127245-A-G
• rs1566667

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 0.795 in 152,128 control chromosomes in the GnomAD database, including 48,946 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 0.79 (48946 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 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: 0.795 AC: 120862 AN: 152010 Hom.: 48942 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.795 AC: 120908 AN: 152128 Hom.: 48946 Cov.: 32 AF XY: 0.791 AC XY: 58835 AN XY: 74356

African (AFR) AF: 0.636 AC: 26382 AN: 41480

American (AMR) AF: 0.826 AC: 12623 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2586 AN: 3472

East Asian (EAS) AF: 0.738 AC: 3809 AN: 5162

South Asian (SAS) AF: 0.700 AC: 3374 AN: 4818

European-Finnish (FIN) AF: 0.860 AC: 9100 AN: 10586

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60209 AN: 68008

Other (OTH) AF: 0.811 AC: 1713 AN: 2112

Alfa AF: 0.852 Hom.: 70701

Bravo AF: 0.790

Asia WGS AF: 0.698 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.50
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs1566667; hg19: chr12-130611790;