17-12664783-G-A

Variant names:

• chr17-12664783-G-A
• rs976906

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 151,996 control chromosomes in the GnomAD database, including 16,375 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 (16375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69973 AN: 151878 Hom.: 16358 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.461 AC: 70039 AN: 151996 Hom.: 16375 Cov.: 32 AF XY: 0.460 AC XY: 34155 AN XY: 74268

African (AFR) AF: 0.471 AC: 19510 AN: 41452

American (AMR) AF: 0.424 AC: 6473 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1745 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1386 AN: 5164

South Asian (SAS) AF: 0.551 AC: 2647 AN: 4806

European-Finnish (FIN) AF: 0.420 AC: 4431 AN: 10548

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.474 AC: 32244 AN: 67980

Other (OTH) AF: 0.473 AC: 1000 AN: 2116

Alfa AF: 0.467 Hom.: 26299

Bravo AF: 0.457

Asia WGS AF: 0.431 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.81
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs976906; hg19: chr17-12568100;