17-12257328-G-A

Variant names:

• chr17-12257328-G-A
• rs8068445

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 0.14 in 152,032 control chromosomes in the GnomAD database, including 1,634 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 0.14 (1634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.25 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: 0.140 AC: 21294 AN: 151916 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0851

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.140 AC: 21321 AN: 152032 Hom.: 1634 Cov.: 32 AF XY: 0.144 AC XY: 10687 AN XY: 74296

African (AFR) AF: 0.109 AC: 4509 AN: 41486

American (AMR) AF: 0.196 AC: 2998 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0851 AC: 295 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1349 AN: 5160

South Asian (SAS) AF: 0.245 AC: 1174 AN: 4792

European-Finnish (FIN) AF: 0.129 AC: 1366 AN: 10570

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9138 AN: 67976

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.141 Hom.: 2786

Bravo AF: 0.142

Asia WGS AF: 0.221 AC: 768 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	1.6
DANN	Benign	0.53
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs8068445; hg19: chr17-12160645;