rs7966485

Variant names:

• chr12-94689566-C-T
• rs7966485

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 0.461 in 151,904 control chromosomes in the GnomAD database, including 16,308 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 0.46 (16308 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70001 AN: 151782 Hom.: 16288 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.461 AC: 70056 AN: 151904 Hom.: 16308 Cov.: 31 AF XY: 0.458 AC XY: 33994 AN XY: 74218

African (AFR) AF: 0.459 AC: 18995 AN: 41408

American (AMR) AF: 0.397 AC: 6059 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1380 AN: 5176

South Asian (SAS) AF: 0.466 AC: 2250 AN: 4824

European-Finnish (FIN) AF: 0.494 AC: 5187 AN: 10502

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33135 AN: 67954

Other (OTH) AF: 0.451 AC: 953 AN: 2112

Alfa AF: 0.476 Hom.: 7354

Bravo AF: 0.454

Asia WGS AF: 0.375 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs7966485; hg19: chr12-95083342;