rs12948783

Variant names:

• chr17-76503318-G-A
• rs12948783

Your query was ambiguous. Multiple possible variants found:

• chr17-76503318-G-A
• chr17-76503318-G-C
• chr17-76503318-G-T

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 0.184 in 152,136 control chromosomes in the GnomAD database, including 2,803 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 0.18 (2803 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27929 AN: 152018 Hom.: 2802 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.184 AC: 27957 AN: 152136 Hom.: 2803 Cov.: 33 AF XY: 0.187 AC XY: 13926 AN XY: 74366

African (AFR) AF: 0.206 AC: 8562 AN: 41492

American (AMR) AF: 0.183 AC: 2798 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3472

East Asian (EAS) AF: 0.104 AC: 540 AN: 5192

South Asian (SAS) AF: 0.406 AC: 1960 AN: 4826

European-Finnish (FIN) AF: 0.141 AC: 1494 AN: 10580

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11135 AN: 67984

Other (OTH) AF: 0.189 AC: 398 AN: 2108

Alfa AF: 0.176 Hom.: 6566

Bravo AF: 0.181

Asia WGS AF: 0.257 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12948783; hg19: chr17-74499400;