17-45392790-G-A

Variant names:

• chr17-45392790-G-A
• rs1230094

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 0.361 in 152,096 control chromosomes in the GnomAD database, including 10,525 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 0.36 (10525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.361 AC: 54810 AN: 151978 Hom.: 10513 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.361 AC: 54861 AN: 152096 Hom.: 10525 Cov.: 33 AF XY: 0.362 AC XY: 26884 AN XY: 74352

African (AFR) AF: 0.493 AC: 20456 AN: 41476

American (AMR) AF: 0.313 AC: 4783 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1157 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5168

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4826

European-Finnish (FIN) AF: 0.294 AC: 3114 AN: 10584

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20367 AN: 67970

Other (OTH) AF: 0.378 AC: 800 AN: 2114

Alfa AF: 0.320 Hom.: 29671

Bravo AF: 0.370

Asia WGS AF: 0.412 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.61
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1230094; hg19: chr17-43470156;