rs9905385

Variant names:

• chr17-61420889-A-G
• rs9905385

Your query was ambiguous. Multiple possible variants found:

• chr17-61420889-A-G
• chr17-61420889-A-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 0.708 in 152,008 control chromosomes in the GnomAD database, including 38,396 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 0.71 (38396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.707 AC: 107435 AN: 151888 Hom.: 38347 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.708 AC: 107546 AN: 152008 Hom.: 38396 Cov.: 31 AF XY: 0.710 AC XY: 52736 AN XY: 74276

African (AFR) AF: 0.796 AC: 32986 AN: 41464

American (AMR) AF: 0.663 AC: 10119 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3472

East Asian (EAS) AF: 0.694 AC: 3572 AN: 5150

South Asian (SAS) AF: 0.625 AC: 3014 AN: 4824

European-Finnish (FIN) AF: 0.737 AC: 7770 AN: 10536

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45412 AN: 67984

Other (OTH) AF: 0.678 AC: 1425 AN: 2102

Alfa AF: 0.726 Hom.: 10241

Bravo AF: 0.707

Asia WGS AF: 0.658 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.020
DANN	Benign	0.40
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs9905385; hg19: chr17-59498250;