rs9303387

Variant names:

• chr17-56627494-G-A
• rs9303387

Your query was ambiguous. Multiple possible variants found:

• chr17-56627494-G-A
• chr17-56627494-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 0.0782 in 122,382 control chromosomes in the GnomAD database, including 848 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 0.078 (848 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• 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 (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.0781 AC: 9559 AN: 122360 Hom.: 845 Cov.: 23

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00948

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0289

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00525

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0782 AC: 9567 AN: 122382 Hom.: 848 Cov.: 23 AF XY: 0.0825 AC XY: 4680 AN XY: 56736

African (AFR) AF: 0.234 AC: 7650 AN: 32736

American (AMR) AF: 0.0397 AC: 383 AN: 9638

Ashkenazi Jewish (ASJ) AF: 0.0289 AC: 96 AN: 3318

East Asian (EAS) AF: 0.148 AC: 599 AN: 4040

South Asian (SAS) AF: 0.0268 AC: 97 AN: 3614

European-Finnish (FIN) AF: 0.0598 AC: 293 AN: 4896

Middle Eastern (MID) AF: 0.0486 AC: 7 AN: 144

European-Non Finnish (NFE) AF: 0.00525 AC: 323 AN: 61492

Other (OTH) AF: 0.0669 AC: 111 AN: 1660

Alfa AF: 0.0226 Hom.: 395

Bravo AF: 0.0763

Asia WGS AF: 0.0690 AC: 239 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	3.0
DANN	Benign	0.82
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs9303387; hg19: chr17-54704855;